Proteopedia - User contributions [en]

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T20:19:48Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase 1=

<StructureSection load='6WF2M' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in euaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Zn_and_water_round_2/8'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/5'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/5'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The configuration of the tunnel and formation of the acyl chain are the basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/4'>carbon 9 and carbon 10</scene> where the double bond is generated. Carbon 8 and Carbon 11 in Stearoyl-CoA are not eclipsed, therefore, the substrate is in the gauche conformation. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/6'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/4'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/4'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/4'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/7'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/4'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> Ming-Jia, Yu and Shi-Lu, Chen From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å ACS Catalysis 2019. DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product <scene name='87/877606/Introduction_image_di-iron/18'>Oleoyl-CoA</scene> in the cis conformation and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T20:16:37Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase 1=

<StructureSection load='6WF2M' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in euaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Zn_and_water_round_2/8'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/5'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/5'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/4'>carbon 9 and carbon 10</scene> where the double bond is generated. Carbon 8 and Carbon 11 in Stearoyl-CoA are not eclipsed, therefore, the substrate is in the gauche conformation. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/6'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/4'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/4'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/4'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/7'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/4'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> Ming-Jia, Yu and Shi-Lu, Chen From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å ACS Catalysis 2019. DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product <scene name='87/877606/Introduction_image_di-iron/18'>Oleoyl-CoA</scene> in the cis conformation and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T20:14:38Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase 1=

<StructureSection load='6WF2M' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in euaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Zn_and_water_round_2/8'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/5'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/5'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/4'>carbon 9 and carbon 10</scene> where the double bond is generated. Carbon 8 and Carbon 11 in Stearoyl-CoA are not eclipsed, therefore, the substrate is in the gauche conformation. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/6'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/7'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/4'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> Ming-Jia, Yu and Shi-Lu, Chen From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å ACS Catalysis 2019. DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product <scene name='87/877606/Introduction_image_di-iron/18'>Oleoyl-CoA</scene> in the cis conformation and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T20:11:59Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase=

<StructureSection load='6WF2M' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in euaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Zn_and_water_round_2/8'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/5'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/5'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/4'>carbon 9 and carbon 10</scene> where the double bond is generated. Carbon 8 and Carbon 11 in Stearoyl-CoA are not eclipsed, therefore, the substrate is in the gauche conformation. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/6'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/7'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/4'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> Ming-Jia, Yu and Shi-Lu, Chen From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å ACS Catalysis 2019. DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product <scene name='87/877606/Introduction_image_di-iron/18'>Oleoyl-CoA</scene> in the cis conformation and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T20:10:30Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2M' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in euaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Zn_and_water_round_2/8'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/5'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/5'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/4'>carbon 9 and carbon 10</scene> where the double bond is generated. Carbon 8 and Carbon 11 in Stearoyl-CoA are not eclipsed, therefore, the substrate is in the gauche conformation. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/6'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/7'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/4'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> Ming-Jia, Yu and Shi-Lu, Chen From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å ACS Catalysis 2019. DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product <scene name='87/877606/Introduction_image_di-iron/18'>Oleoyl-CoA</scene> in the cis conformation and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T20:07:10Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2M' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in euaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/5'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/4'>carbon 9 and carbon 10</scene> where the double bond is generated. Carbon 8 and Carbon 11 in Stearoyl-CoA are not eclipsed, therefore, the substrate is in the gauche conformation. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/6'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> Ming-Jia, Yu and Shi-Lu, Chen From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å ACS Catalysis 2019. DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product <scene name='87/877606/Introduction_image_di-iron/18'>Oleoyl-CoA</scene> in the cis conformation and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T20:04:31Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2M' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in euaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/6'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> Ming-Jia, Yu and Shi-Lu, Chen From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å ACS Catalysis 2019. DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product <scene name='87/877606/Introduction_image_di-iron/18'>Oleoyl-CoA</scene> in the cis conformation and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T20:03:00Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2M' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in euaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> Ming-Jia, Yu and Shi-Lu, Chen From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å ACS Catalysis 2019. DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product <scene name='87/877606/Introduction_image_di-iron/18'>Oleoyl-CoA</scene> in the cis conformation and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T19:42:06Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2M' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in euaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> Ming-Jia, Yu and Shi-Lu, Chen From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å ACS Catalysis 2019. DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA in the gauche conformation) and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T19:40:18Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2M' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in euaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> Ming-Jia, Yu and Shi-Lu, Chen From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å ACS Catalysis 2019. DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T19:35:35Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2M' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in euaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> McKinley and Durand awesome paper. DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T19:31:14Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name="Shen">PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T19:13:37Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_correct_one/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T19:11:47Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/6'>N261 </scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T19:10:06Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877606/N261_update_ajd/1'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T19:07:06Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/6'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:54:59Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found [http://www.rcsb.org/structure/4ZYO (4ZYO)]. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/5'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:52:46Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/5'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded.]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3)<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules<ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:51:22Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/5'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==
*Abbey Wells
*Josey McKinley
*Anthony Durand

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:49:51Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one/3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/5'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:48:30Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/5'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:45:40Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices, arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref>. A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>. The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:43:43Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref> .

A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at position 835 of the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:42:29Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.

The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref> .

A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:41:27Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref>.The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref> .

A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:41:03Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
SCD1’s role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease <ref name="Ntambi">PMID: 14654089</ref> .
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present <ref name="ALJohani">PMID: 29089222</ref> .

A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:37:16Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Substrate ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:34:57Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as they have similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn in coordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:33:36Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl CoA] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK 4YMK] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid Oleic Acid] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 6WF2]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as it has similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn incoordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:31:41Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [http://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [http://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [http://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [http://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as it has similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn incoordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:28:25Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as it has similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn incoordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:27:25Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as it has similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn incoordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/4'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/4'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/5'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:26:40Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as it has similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn incoordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and polar atoms such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/4'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/5'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via hydrogen bonds. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:22:36Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as it has similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn incoordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

=== Binding of Substrate ===
Stearoyl-CoA is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty acyl-CoA. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and many atoms of Nitrogen, oxygen, and sulfur. The fatty acid tail is a 17-carbon chain which reaches into the interior of the protein. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached via <scene name='87/877602/Hydrophillic_top/2'>Hydrophillic Top</scene> groups that include R151, D152, and K185. The rest of the exterior of the substrate is attached via <scene name='87/877602/Hydrophillic_bottom_labeled/2'>Hydrophillic Bottom</scene> groups that include R184, N144, and N71. The fatty acid chain dives into the interior of the enzyme. The acyl chain is enclosed in a tunnel (24 ang) buried in the cytosolic domain. The geometry of the tunnel and formormation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction. The chain is kinked at carbon 9-carbon 10 where the double bond is generated. The <scene name='87/877602/Full_kink/2'>Kink</scene> is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink/2'>W149, T257, and Q143</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149. These residues are directly below the kink and will be hydrolyzed when the substrate is ready to be released. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/Trp258/2'>Trp258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:18:01Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as it has similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn incoordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The configuration of the tunnel and location of the acyl chain are the basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:15:29Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as it has similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn incoordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref>.
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:14:43Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as it has similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn incoordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==
A mutation in one of these nine histidines causes the enzyme to become nonfunctional.<ref name="Bai">PMID:26098370</ref> . The inactivation of SCD1 also has been known to inhibit cancer cell growth <ref name="Shen">PMID:32470559</ref> .
The inactivation of SCD1 is also commonly caused by a frameshift mutation by the addition of a proline at the 279th position. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/4'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 5th exon at the 835 position SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean during their lifespan due to decreased triglyceride synthesis connected to the loss of SCD1 function <ref name="Lu">PMID: 15278437</ref>

</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-27T18:13:16Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

Using X-ray crystallography, three structures of SCD have been found, differing only in their dimetal center and organism of origin. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/4'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/4'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as it has similar characteristics including charge and ionic radius size <ref name=”Shen”>PMID:32470559</ref> .However, Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is common of Fe ion coordination <ref name="Bai">PMID:26098370</ref> More recently, the structure of the human SCD1 (hSCD1) protein was found. This structure was found with Zn incoordination; however, the researchers agree that iron is the true metal in the dimetal center. <ref name=”Wang”>PMID:26098317</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-26T00:27:45Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid] (Fig 1), an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism for the SCD1 catalyzed desaturation reaction involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron originating from the electron transport chain (Fig 2) react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-26T00:16:11Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-20T20:17:27Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism which involving a molecular oxygen, water, two protons, and two electrons (2e-). <ref name="Yu"> DOI:10.1021/acscatal.9b00456 </ref>

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-20T20:16:10Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism which involving a molecular oxygen, water, two protons, and two electrons (2e-)<ref name="Yu">doi:10.1021/acscatal.9b00456</ref>.

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-20T20:14:04Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism which involving a molecular oxygen, water, two protons, and two electrons (2e-)<ref name="MingJia">doi:10.1021/acscatal.9b00456</ref>.

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-20T20:13:01Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism which involving a molecular oxygen, water, two protons, and two electrons (2e-)<ref name="Ming-Jia">doi:10.1021/acscatal.9b00456</ref>.

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-20T20:10:26Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism which involving a molecular oxygen, water, two protons, and two electrons (2e-)<ref name="Ming-Jia">doi 10.1021/acscatal.9b00456 </ref>.

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-20T20:08:13Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism which involving a molecular oxygen, water, two protons, and two electrons (2e-)<ref name="Ming-Jia">doi:10.1021</ref>.

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-20T20:06:24Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism which involving a molecular oxygen, water, two protons, and two electrons (2e-)<ref name="Ming-Jia Yu and Shi-Lu Chen">doi:10.1021</ref>.

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-20T20:03:59Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism which involving a molecular oxygen, water, two protons, and two electrons (2e-)<ref name="Ming-Jia Yu and Shi-Lu Chen">doi:10.1021/acscatal.9b00456</ref>.

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-20T20:01:57Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism which involving a molecular oxygen, water, two protons, and two electrons (2e-)<ref name="Ming-Jia Yu and Shi-Lu Chen">DOI: 10.1021/acscatal.9b00456</ref>.

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==

User:Anthony Jude Durand Jr./Sandbox1

2021-04-20T19:58:51Z

Anthony Jude Durand Jr.:

=Stearoyl CoA Desaturase from Mus ''musculus''=

<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Coverpageimage/3'>

== Introduction ==
Stearoyl-CoA Desaturase is an enzyme essential for the biosynthesis of monosaturated fatty acids from saturated fatty acids <ref name="Paton">doi: 10.1152/ajpendo.90897.2008</ref>. SCD catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol <ref name="Bai">PMID:26098370</ref>.
SCD is highly conserved in eukaryotes and has different gene isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD isoform discussed in this page is [http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] found in mice. SCD is believed to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago <ref name="Filipe">doi: 10.1186/1471-2148-11-132</ref>. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography <ref name="Bai">PMID:26098370</ref>.
[[Image:OverallReaction.png|800px|center|thumb| [Figure 1] Desaturation Reaction Catalyzed by SCD1: Stearoyl-CoA (left) is converted to oleoyl-CoA (right) through the introduction of a double bond between C9 and C10.]]

== Structure ==

=== Overall Structure ===
[[Image:SCD1_ETC.png|525px|right|thumb| [Figure 2] SCD1 and Electron Transport Chain: Two electrons from NADH (left) are transported to Cytochrome B5 Reductase (Green) then Cytochrome B5 (Blue) and finally to SCD1 (Right) where they can be used in the desaturation reaction. Cytochrome B5 Reductase and Cytochrome B5 are bound to the cytosolic side of the ER membrane whereas SCD1 is embedded within the membrane of the ER. ]]SCD1 is an integral membrane protein embedded within the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane [http://en.wikipedia.org/wiki/Alpha_helix alpha helices], arranged in a cone-like shape. The cytosolic domain of the enzyme consists of 11 alpha helices and contains the carboxy and amino termini <ref name="Bai">PMID:26098370</ref>.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877602/C9_and_c10/2'>carbon 9 and carbon 10</scene> of Stearoyl-CoA.

=== Binding of Substrate ===
[http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty [http://en.wikipedia.org/wiki/Acyl-CoA#:~:text=Acyl%2DCoA%20is%20a%20group,forming%20several%20equivalents%20of%20ATP. acyl-CoA]. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and [http://en.wikipedia.org/wiki/Chemical_polarity#:~:text=In%20chemistry%2C%20polarity%20is%20a,electronegativity%20between%20the%20bonded%20atoms polar atoms] such as of nitrogen, oxygen, and sulfur. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached by the residues <scene name='87/877602/Hydrophillic_top_t/3'>R151, D152, K185</scene>. The remaining exterior of the substrate is attached by the residues <scene name='87/877602/Hydrophillic_bottom_labeled_t/4'>N144, N71, R184</scene> <ref name="Bai">PMID:26098370</ref>. All the conserved residues are attached to the Stearoyl-CoA via [http://en.wikipedia.org/wiki/Hydrogen_bond#:~:text=A%20hydrogen%20bond%20(often%20informally,donor%20(Dn)%E2%80%94and%20another hydrogen bonds]. The fatty acid tail of Stearoyl-CoA is a 17-carbon chain which reaches into the interior of the protein. The fatty acid chain dives into the interior hydrophobic tunnel which is long, narrow, and approximately 24 Angstroms long <ref name="Bai">PMID:26098370</ref>. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction <ref name="Bai">PMID:26098370</ref>.
=== Kink of Chain ===
The chain is kinked at <scene name='87/877602/C9_and_c10/3'>carbon 9 and carbon 10</scene> where the double bond is generated. The kink is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: <scene name='87/877602/Kink_build/3'>T257, Q143, W149</scene>. T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149 <ref name="Bai">PMID:26098370</ref>. These residues are directly below the kink and will be hydrolyzed when the enzymatic product is ready to be released. Specifically, if the hydrogen bond between T257 and Q143 is broken, a large opening would allow for the product to be released into the bilayer <ref name="Bai">PMID:26098370</ref>. The residue that is directly hydrogen bonded to the chain is <scene name='87/877602/W258/3'>W258</scene>. This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site. The enzyme will be effective on acyl chains that are between 17 to 19 carbons long. The residue that has a role in determining substrate length is <scene name='87/877602/Cap/4'>Y104</scene>. Y104 is a capping residue that has approximately 4 [http://en.wikipedia.org/wiki/Angstrom Angstroms] between its' hydroxyl oxygen and the end of the chain <ref name="Bai">PMID:26098370</ref>.

=== Active Site ===
Using X-ray crystallography, two structures of SCD have been found, differing only in their dimetal center. One structure includes the substrate [https://en.wikipedia.org/wiki/Stearoyl-CoA (Stearoyl CoA)] a water molecule, and two <scene name='87/877627/Just_zn_but_zoomed_out/3'>zinc </scene> ions in the center [https://www.rcsb.org/structure/4YMK (4YMK)] <ref name="Bai">PMID:26098370</ref>
A second structure found more recently includes the product [https://en.wikipedia.org/wiki/Oleic_acid (Oleic Acid)] and two <scene name='87/877627/Zoomed_out_fe/3'>iron </scene> ions in the center [https://www.rcsb.org/structure/6WF2 (6WF2)]. When testing the Zn centered structure, the enzyme was found to be inactive <ref name="Shen">PMID:32470559</ref>
The Zn ions serve as a surrogate for Fe as Zn did not display its typical coordination geometry, tetrahedral; instead, it displayed octahedral geometry which is typically of Fe ion coordination <ref name="Bai">PMID:26098370</ref>
For the images and links below, the zinc ion centered structure will be used as it includes the substrate, even though iron is confirmed as the dimetal center.

The dimetal center is essential to the catalytic activity, as previously demonstrated in the mechanism above. The <scene name='87/877627/Zn_with_measurement/3'>zinc</scene> ions are 6.4 angstroms apart <ref name="Bai">PMID:26098370</ref>
The ions sit above the kink created by C9 and C10 of the substrate within the active site. The ions are held into the active site through the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> <ref name="Kikuchi">PMID: 31838050</ref> . The nine coordinating His residues stabilize the ions into the active site forming a non-heme prosthetic group <ref name="Kikuchi">PMID: 31838050</ref> . The His box is highly conserved among the isoforms of SCD <ref name="Shen">PMID:32470559</ref> .
The <scene name='87/877627/Zn2/3'>ion</scene> closest to C10 of the substrate is 4.7 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> . This ion is coordinated by five histidine residues. The <scene name='87/877627/Zn1/3'>ion</scene> closest to C9 of the substrate is 5.2 angstroms away from this carbon <ref name="Bai">PMID:26098370</ref> This ion is coordinated with four histidine residues and one water molecule. The <scene name='87/877627/Zn_and_water_round_2/4'>water</scene> is in coordination to the zinc ion closest to it. It occupies the fifth <scene name='87/877627/His_box_w_o_labels/3'>coordination site</scene>.

Residues around the periphery hydrogen bond to the His box to stabilize it. These residues include <scene name='87/877627/D165_correct_one/5'>D165</scene> <scene name='87/877627/E291_correct_one3'>E291</scene> and <scene name='87/877627/E161_correct_one/3'>E161 </scene> <ref name="Bai">PMID:26098370</ref> . Another residue that stabilizes the active site is <scene name='87/877627/N261_correct_one/4'>N261</scene>. This residue hydrogen bonds to the water molecule <ref name="Bai">PMID:26098370</ref> .

The His box and periphery residues stabilize the dimetal center and make up the <scene name='87/877627/Active_site_round_3_but_labels/3'>active site</scene> of the enzyme.This allows for the proposed above mechanism to be carried out.

== Mechanism ==

[[Image:SCDMech.jpg|550px|thumb|left| [Figure 3] Proposed Mechanism: The SCD1-catalyzed desaturation reaction involves a molecular oxygen, water molecule, two protons and electrons, and two iron ions within the enzyme core which through a series of redox reactions and hydrogen transfers introduce a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid. The penta- and tetra-coordinated irons within the enzyme core are represented by Fe(A) and Fe(B) respectively. All electron pushing steps are shown with reactive groups color coded. ]]

Although the precise mechanism behind SCD1 catalysis is still unknown, several mechanisms have been proposed. In a recent article by Yu and Chen, they propose a novel mechanism which involving a molecular oxygen, water, two protons, and two electrons (2e-)<ref name="Paton">DOI: 10.1021/acscatal.9b00456</ref>.

In the first step of the proposed mechanism, water and a molecular oxygen bind to the penta- and tetra-coordinated irons in the active site of SCD1, Fe(A) and Fe(B) respectively (Fig 3). This binding results in the transfer of an electron from the tetra-coordinated iron to the molecular oxygen forming an iron(III)-dioxygen radical species. This is followed by a proton transfer from the iron(II) bound water to the iron(III) bound di-oxygen radical which results in the formation of iron(II)-hydroxyl radical and iron(II)-peroxyl radical intermediates (Fig 3).

One electron and one proton, originating from the electron transport chain, are then incorporated into the reaction resulting in the protonation of the hydroxyl radical to form an iron(II)-water intermediate. In this step the iron(II)-peroxyl radical is coordinated by the iron(II)-water and the tetra-coordinated iron (Fig 3).This step is quickly followed by the dissociation of the O-O bond of the peroxyl radical where one of the hydrogens from the iron(II)-water is transferred to the radical oxygen on the iron(II)-peroxyl resulting in the formation of a triple-hydroxyl intermediate (Fig 3) with the penta-coordinated iron being converted to iron(III).This intermediate then undergoes a hydrogen transfer where a hydrogen from the one of the hydroxyl groups on the dihydroxyl intermediate is transferred to the other hydroxyl group on the intermediate. This results in the formation of a water molecule coordinated between a newly formed high-valent iron(IV)=O and the iron(III)-hydroxyl (Fig 3).

Following the formation of the high-valent iron(IV)=O, the first hydrogen abstraction from the substrate occurs with C9 hydrogen on the substrate being abstracted by the iron(IV)=O forming a C9 radical on the substrate and converting the high-valent iron(IV)=O to a iron(III)-hydroxyl (Fig 3). This is quickly followed by another hydrogen abstraction from the penta-coordinated iron(III)-hydroxyl which results in the formation of a double bond between C9 and C10 and converting the penta-coordinated iron(III)-hydroxyl to iron(II)-water. Once the product has been formed, another proton and electron react with the iron(III)-hydroxyl intermediate to form iron(II)-water. At this point, the enzyme-substrate complex dissociates with the release of the product (Oleoyl-CoA) and three water molecules.

==Biological Significance ==

SCD1 role in converting stearoyl CoA, a saturated fatty acid, to oleic acid, a monounsaturated fatty acid, is essential in lipid metabolism. Fluxes in the ratio of saturated fatty acids to monounsaturated fatty acids can be connected to many different disease states, including obesity, diabetes, cancer, and cardiovascular disease (Ntambi).
The inactivation of SCD1 has been known to have combative effects on obesity and diabetes. Increased levels of oleic acid are present in both obesity and diabetes; therefore, inactivating the enzyme will allow for decreased amounts of product present (Ahmed). The inactivation of SCD1 is most commonly seen as a mutation to any of the nine histidine residues present in the <scene name='87/877627/His_box_w_o_water/2'>His box</scene> (Yonghong). A mutation in any of these positions leads to a nonfunctional enzyme. The inactivation of SCD1 also has been known to inhibit cancer cell growth (Shen).
The inactivation of SCD1 is also commonly caused by the insertion of a proline at position 279. In the wild type SCD1 protein, this position contains an <scene name='87/877627/R279/3'>arginine residue</scene>. A ‘CCC’ codon is inserted into the 835 position of exon 5 in the SCD1 gene. This mutation results in a loss of function of SCD1. This study was done using a mouse model. In mice with this mutation, hair loss, similar to alopecia, occurs. The mice were also found to be lean throughout their lifespan due to reduced triglyceride synthesis connected to the loss of SCD1 function (Y Lu).
</StructureSection>

== References ==

<references/>

==Student Contributors==