https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Joseph+ThomasProteopedia - User contributions [en]2026-10-02T12:18:50ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2395754Sandbox Reserved 10662015-04-17T17:53:26Z<p>Joseph Thomas: </p>
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== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as <scene name='69/694233/General_pic/1'>FadD13</scene>, is unique within its class of FadD proteins in regards to its ability to house [https://en.wikipedia.org/wiki/Lipid lipid] substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose an interesting structural dilemma to the enzyme. FadD13 differs from typical integral membrane fatty acyl-CoA synthetases in that FadD13 exists as a [https://en.wikipedia.org/wiki/Peripheral_membrane_protein peripheral membrane protein]. This key feature provides a mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses many key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The <scene name='69/694233/Hydrophobic_tunnel/2'>hydrophobic tunnel</scene> of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 4).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutation of the highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, <scene name='69/694233/Ser_404/1'>Serine 404</scene> was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably [https://en.wikipedia.org/wiki/Mycolic_acid mycolic acids], which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
Drugs developed thus far that have been shown to inhibit mycolic acid biosynthesis are: [https://en.wikipedia.org/wiki/Isoniazid isoniazid], [https://en.wikipedia.org/wiki/Ethionamide ethionamide], [https://en.wikipedia.org/wiki/Thiocarlide thiocarlide], thiolactomycin, and [https://en.wikipedia.org/wiki/Triclosan triclosan]. <ref name="Drug Inhibitors"/> Additionally, [https://en.wikipedia.org/wiki/Pyrazinamide pyrazinamide] was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
<br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Lipid Lipids] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/peripheral_membrane_protein Peripheral Membrane Protein] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Ethionamide Ethionamide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Isoniazid Isoniazid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Thiocarlide Thiocarlide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Triclosan Triclosan]<br />
<br />
[https://en.wikipedia.org/wiki/Pyrazinamide Pyrazinamide] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2395751Sandbox Reserved 10662015-04-17T17:50:40Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as <scene name='69/694233/General_pic/1'>FadD13</scene>, is unique within its class of FadD proteins in regards to its ability to house [https://en.wikipedia.org/wiki/Lipid lipid] substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose an interesting structural dilemma to the enzyme. FadD13 differs from typical integral membrane fatty acyl-CoA synthetases in that FadD13 exists as a [https://en.wikipedia.org/wiki/Peripheral_membrane_protein peripheral membrane protein]. This key feature provides a mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses many key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The <scene name='69/694233/Hydrophobic_tunnel/2'>hydrophobic tunnel</scene> of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 4).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutation of the highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, <scene name='69/694233/Ser_404/1'>Serine 404</scene> was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably [https://en.wikipedia.org/wiki/Mycolic_acid mycolic acids], which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
Drugs developed thus far that have been shown to inhibit mycolic acid biosynthesis are: [https://en.wikipedia.org/wiki/Isoniazid isoniazid], [https://en.wikipedia.org/wiki/Ethionamide ethionamide], [https://en.wikipedia.org/wiki/Thiocarlide thiocarlide], thiolactomycin, and [https://en.wikipedia.org/wiki/Triclosan triclosan]. <ref name="Drug Inhibitors"/> Additionally, [https://en.wikipedia.org/wiki/Pyrazinamide pyrazinamide] was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Lipid Lipids] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/peripheral_membrane_protein Peripheral Membrane Protein] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Ethionamide Ethionamide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Isoniazid Isoniazid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Thiocarlide Thiocarlide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Triclosan Triclosan]<br />
<br />
[https://en.wikipedia.org/wiki/Pyrazinamide Pyrazinamide] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2395750Sandbox Reserved 10662015-04-17T17:46:29Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as <scene name='69/694233/General_pic/1'>FadD13</scene>, is unique within its class of FadD proteins in regards to its ability to house [https://en.wikipedia.org/wiki/Lipid lipid] substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose an interesting structural dilemma to the enzyme. FadD13 differs from typical integral membrane fatty acyl-CoA synthetases in that FadD13 exists as a [https://en.wikipedia.org/wiki/Peripheral_membrane_protein peripheral membrane protein]. This key feature provides a mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses many key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The <scene name='69/694233/Hydrophobic_tunnel/2'>hydrophobic tunnel</scene> of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 4).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutation of the highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably [https://en.wikipedia.org/wiki/Mycolic_acid mycolic acids], which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
Drugs developed thus far that have been shown to inhibit mycolic acid biosynthesis are: [https://en.wikipedia.org/wiki/Isoniazid isoniazid], [https://en.wikipedia.org/wiki/Ethionamide ethionamide], [https://en.wikipedia.org/wiki/Thiocarlide thiocarlide], thiolactomycin, and [https://en.wikipedia.org/wiki/Triclosan triclosan]. <ref name="Drug Inhibitors"/> Additionally, [https://en.wikipedia.org/wiki/Pyrazinamide pyrazinamide] was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Lipid Lipids] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/peripheral_membrane_protein Peripheral Membrane Protein] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Ethionamide Ethionamide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Isoniazid Isoniazid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Thiocarlide Thiocarlide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Triclosan Triclosan]<br />
<br />
[https://en.wikipedia.org/wiki/Pyrazinamide Pyrazinamide] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2395748Sandbox Reserved 10662015-04-17T17:42:53Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as <scene name='69/694233/General_pic/1'>FadD13</scene>, is unique within its class of FadD proteins in regards to its ability to house [https://en.wikipedia.org/wiki/Lipid lipid] substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose an interesting structural dilemma to the enzyme. FadD13 differs from typical integral membrane fatty acyl-CoA synthetases in that FadD13 exists as a [https://en.wikipedia.org/wiki/Peripheral_membrane_protein peripheral membrane protein]. This key feature provides a mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses many key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The <scene name='69/694233/Hydrophobic_tunnel/1'>hydrophobic tunnel</scene> of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 4).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutation of the highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably [https://en.wikipedia.org/wiki/Mycolic_acid mycolic acids], which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
Drugs developed thus far that have been shown to inhibit mycolic acid biosynthesis are: [https://en.wikipedia.org/wiki/Isoniazid isoniazid], [https://en.wikipedia.org/wiki/Ethionamide ethionamide], [https://en.wikipedia.org/wiki/Thiocarlide thiocarlide], thiolactomycin, and [https://en.wikipedia.org/wiki/Triclosan triclosan]. <ref name="Drug Inhibitors"/> Additionally, [https://en.wikipedia.org/wiki/Pyrazinamide pyrazinamide] was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Lipid Lipids] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/peripheral_membrane_protein Peripheral Membrane Protein] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Ethionamide Ethionamide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Isoniazid Isoniazid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Thiocarlide Thiocarlide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Triclosan Triclosan]<br />
<br />
[https://en.wikipedia.org/wiki/Pyrazinamide Pyrazinamide] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2395747Sandbox Reserved 10662015-04-17T17:40:02Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as <scene name='69/694233/General_pic/1'>FadD13</scene>, is unique within its class of FadD proteins in regards to its ability to house [https://en.wikipedia.org/wiki/Lipid lipid] substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose an interesting structural dilemma to the enzyme. FadD13 differs from typical integral membrane fatty acyl-CoA synthetases in that FadD13 exists as a [https://en.wikipedia.org/wiki/Peripheral_membrane_protein peripheral membrane protein]. This key feature provides a mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses many key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 4).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutation of the highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably [https://en.wikipedia.org/wiki/Mycolic_acid mycolic acids], which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
Drugs developed thus far that have been shown to inhibit mycolic acid biosynthesis are: [https://en.wikipedia.org/wiki/Isoniazid isoniazid], [https://en.wikipedia.org/wiki/Ethionamide ethionamide], [https://en.wikipedia.org/wiki/Thiocarlide thiocarlide], thiolactomycin, and [https://en.wikipedia.org/wiki/Triclosan triclosan]. <ref name="Drug Inhibitors"/> Additionally, [https://en.wikipedia.org/wiki/Pyrazinamide pyrazinamide] was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Lipid Lipids] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/peripheral_membrane_protein Peripheral Membrane Protein] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Ethionamide Ethionamide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Isoniazid Isoniazid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Thiocarlide Thiocarlide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Triclosan Triclosan]<br />
<br />
[https://en.wikipedia.org/wiki/Pyrazinamide Pyrazinamide] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2395744Sandbox Reserved 10662015-04-17T17:36:34Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as <scene name='69/694233/General_pic/1'>FadD13</scene>, is unique within its class of FadD proteins in regards to its ability to house [https://en.wikipedia.org/wiki/Lipid lipid] substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose an interesting structural dilemma to the enzyme. FadD13 differs from typical integral membrane fatty acyl-CoA synthetases in that FadD13 exists as a [https://en.wikipedia.org/wiki/Peripheral_membrane_protein peripheral membrane protein]. This key feature provides a mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses many key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 4).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutation of the highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably [https://en.wikipedia.org/wiki/Mycolic_acid mycolic acids], which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
Drugs developed thus far that have been shown to inhibit mycolic acid biosynthesis are: [https://en.wikipedia.org/wiki/Isoniazid isoniazid], ethionamide, isoxyl, thiolactomycin, and triclosan. <ref name="Drug Inhibitors"/> Additionally, [https://en.wikipedia.org/wiki/Pyrazinamide pyrazinamide] was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Lipid Lipids] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/peripheral_membrane_protein Peripheral Membrane Protein] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Pyrazinamide Pyrazinamide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Isoniazid Isoniazid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2395743Sandbox Reserved 10662015-04-17T17:35:48Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as <scene name='69/694233/General_pic/1'>FadD13</scene>, is unique within its class of FadD proteins in regards to its ability to house [https://en.wikipedia.org/wiki/Lipid lipid] substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose an interesting structural dilemma to the enzyme. FadD13 differs from typical integral membrane fatty acyl-CoA synthetases in that FadD13 exists as a [https://en.wikipedia.org/wiki/Peripheral_membrane_protein peripheral membrane protein]. This key feature provides a mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses many key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 4).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutation of the highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic acids, which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
Drugs developed thus far that have been shown to inhibit mycolic acid biosynthesis are: [https://en.wikipedia.org/wiki/Isoniazid isoniazid], ethionamide, isoxyl, thiolactomycin, and triclosan. <ref name="Drug Inhibitors"/> Additionally, [https://en.wikipedia.org/wiki/Pyrazinamide pyrazinamide] was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Lipid Lipids] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/peripheral_membrane_protein Peripheral Membrane Protein] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Pyrazinamide Pyrazinamide] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Isoniazid Isoniazid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2395740Sandbox Reserved 10662015-04-17T17:34:24Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as <scene name='69/694233/General_pic/1'>FadD13</scene>, is unique within its class of FadD proteins in regards to its ability to house lipid substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose an interesting structural dilemma to the enzyme. FadD13 differs from typical integral membrane fatty acyl-CoA synthetases in that FadD13 exists as a [https://en.wikipedia.org/wiki/Peripheral_membrane_protein peripheral membrane protein]. This key feature provides a mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses many key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 4).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutation of the highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic acids, which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
Drugs developed thus far that have been shown to inhibit mycolic acid biosynthesis are: [https://en.wikipedia.org/wiki/Isoniazid isoniazid], ethionamide, isoxyl, thiolactomycin, and triclosan. <ref name="Drug Inhibitors"/> Additionally, [https://en.wikipedia.org/wiki/Pyrazinamide pyrazinamide] was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/peripheral_membrane_protein Peripheral Membrane Protein] Wikipedia page<br />
<br />
https://en.wikipedia.org/wiki/Pyrazinamide Pyrazinamide] Wikipedia page<br />
<br />
https://en.wikipedia.org/wiki/Isoniazid Isoniazid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2395739Sandbox Reserved 10662015-04-17T17:33:03Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as <scene name='69/694233/General_pic/1'>FadD13</scene>, is unique within its class of FadD proteins in regards to its ability to house lipid substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose an interesting structural dilemma to the enzyme. FadD13 differs from typical integral membrane fatty acyl-CoA synthetases in that FadD13 exists as a [https://en.wikipedia.org/wiki/Peripheral_membrane_protein peripheral Membrane Protein]. This key feature provides a mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses many key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 4).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutation of the highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic acids, which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
Drugs developed thus far that have been shown to inhibit mycolic acid biosynthesis are: [https://en.wikipedia.org/wiki/Isoniazid isoniazid], ethionamide, isoxyl, thiolactomycin, and triclosan. <ref name="Drug Inhibitors"/> Additionally, https://en.wikipedia.org/wiki/Pyrazinamide pyrazinamide] was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/peripheral_membrane_protein Peripheral Membrane Protein] Wikipedia page<br />
<br />
https://en.wikipedia.org/wiki/Pyrazinamide Pyrazinamide] Wikipedia page<br />
<br />
https://en.wikipedia.org/wiki/Isoniazid Isoniazid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2395737Sandbox Reserved 10662015-04-17T17:29:16Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as <scene name='69/694233/General_pic/1'>FadD13</scene>, is unique within its class of FadD proteins in regards to its ability to house lipid substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose an interesting structural dilemma to the enzyme. FadD13 differs from typical integral membrane fatty acyl-CoA synthetases in that FadD13 exists as a peripheral membrane protein. This key feature provides a mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses many key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 4).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutation of the highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic acids, which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
Drugs developed thus far that have been shown to inhibit mycolic acid biosynthesis are: isoniazid, ethionamide, isoxyl, thiolactomycin, and triclosan. <ref name="Drug Inhibitors"/> Additionally, pyrazinamide was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2395735Sandbox Reserved 10662015-04-17T17:26:36Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class of FadD proteins in regards to its ability to house lipid substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose an interesting structural dilemma to the enzyme. FadD13 differs from typical integral membrane fatty acyl-CoA synthetases in that FadD13 exists as a peripheral membrane protein. This key feature provides a mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses many key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 4).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutation of the highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic acids, which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
Drugs developed thus far that have been shown to inhibit mycolic acid biosynthesis are: isoniazid, ethionamide, isoxyl, thiolactomycin, and triclosan. <ref name="Drug Inhibitors"/> Additionally, pyrazinamide was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393699Sandbox Reserved 10662015-04-10T00:57:32Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class of FadD proteins in regards to its ability to house lipid substrates longer than itself. These lipid substrates are very-long-chain fatty acids between lengths C22 –C26, which is up to the maximum length tested. <ref name="Our Paper"/> The significance of theses very-long-chain fatty acids lies in their importance to mycolic acid synthesis by ''Mycobacterium tuberculosis'' ''(M. tb)''. Mycolic acids compose part of the cell wall of ''(M. tb)''. FadD13, an activator of mycolic acids, has been identified as key component in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
There are four main groups of FadD enzymes categorized on their ability to accommodate different length substrates: short (C2-C4), medium (C4-C12), long (C12-C22), and very long (C22-C26).<ref name="Our Paper"/> Most FadD class proteins exist as integral membrane proteins, involved in both the activation of fatty acids and other hydrophobic substrates in addition to the transport of these lipids into the cell. However, substrates longer than the enzyme itself, like these very-long-chain fatty acids, pose and interesting structural dilemma to the enzyme. In order for FadD13 to accommodate these very long substrates, it differs structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key to the mechanistic basis for FadD13’s activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|right|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme upon the binding of ATP, coenzyme A is able to bind to its active site and react with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13's attachment to the membrane via electrostatic interactions in the N-terminal domain is coupled with the presence of a hydrophobic tunnel located centrally in this same domain. This method of attachment, with the alignment of the hydrophobic tunnel to the membrane, allows the extension of these very-long-chain fatty acids to enter FadD13 from the membrane (Figure 1). Of importance to the passage of these fatty acid substrates into FadD13 resides in the presence of an arginine rich lid-loop, located at the top of the hydrophobic tunnel and embedded in the membrane. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are capable of transportation from the membrane into the enzyme (Figure 1). <br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain houses the main key structural features involved in fatty acid activation, but ultimately it is the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site of FadD13 (Figure 1). <br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 3).<ref name="Our Paper"/> Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
<br />
== Active Site ==<br />
The FadD13 active site is composed of positively charged regions which account for the attraction and binding of hydrophobic substrates to this region (Figure 3). The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/> <br />
<br />
Mutational studies showed that highly conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change after the initial binding of ATP.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic acids, which are known to play a crucial role in the pathogenesis of ''(M. tb)'' <ref name="molecular studies"/> The mycolic acid biosynthetic pathway has been proposed to involve five distinct stages, the first of which is the synthesis of C20 to C26 straight-chain saturated fatty acids activated by FadD13. <ref name="Drug Inhibitors">PMID: 12164478</ref> For this reason, current research has focused on inhibitors to disrupt the initiation of this biosynthetic pathway of mycolic acids in ''(M. tb)''.<br />
<br />
== Current Treatment ==<br />
The drugs developed thus far that have shown to inhibit mycolic acid biosynthesis are: isoniazid, ethionamide, isoxyl, thiolactomycin, and triclosan. <ref name="Drug Inhibitors"/> Additionally, pyrazinamide was shown to inhibit fatty acid synthase type I which is involved in providing a precursor necessary for fatty acid elongation to long-chain mycolic acids. <ref name="Drug Inhibitors"/> Treatment for active cases of tuberculosis include the simultaneous therapeutic use of two or more frontline drugs: isoniazid, ethambutol, rifampicin and pyrazinamide. <ref name="molecular studies"/><br />
<br />
== Future Research ==<br />
While currently there are no specific drug targets for FadD13, a better understanding of key residues involved in the activation of very-long-chain fatty acids is a promising start to developing new drug targets for ''(M. tb)''. Recent studies have shown the ''mymA'' operon, which is involved in the maintenance of ''(M. tb)'' cell wall architecture, and which codes for the enzyme FadD13, is up-regulated under acidic conditions. <ref name="molecular studies"/> Functional loss of the ''mymA'' operon resulted in increased drug sensitivity and death of the pathogen; therefore any drugs that can can target this operon will be effective at fighting tuberculosis. <ref name="molecular studies"/><br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393463Sandbox Reserved 10662015-04-09T02:07:01Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane.<ref name="Our Paper"/> This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
FadD13 has be identified as key to the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 3).<ref name="Our Paper"/> <br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
Mutational studies showed that high conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic acids, which are known to play a crucial role in pathogenesis of ''(M. tb)'' <ref name="molecular studies"/>.<br />
<br />
== Relevance of key mutational studies to the understanding and development of new inhibitors for FadD13 ==<br />
<br />
<ref name="residue paper"/><br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393460Sandbox Reserved 10662015-04-09T02:03:58Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane.<ref name="Our Paper"/> This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
FadD13 has be identified as key to the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 3).<ref name="Our Paper"/> <br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
Mutational studies showed that high conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic aicds, which are known to play a crucial role in pathogenesis of ''(M. tb)'' <ref name="molecular studies"/>.<br />
<br />
== Relevance of key mutational studies to the understanding and development of new inhibitors for FadD13 ==<br />
<br />
<ref name="residue paper"/><br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393457Sandbox Reserved 10662015-04-09T01:57:29Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane.<ref name="Our Paper"/> This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
FadD13 has be identified as key to the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 3).<ref name="Our Paper"/> <br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
Mutational studies showed that high conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic aicds, which are known to play a crucial role in pathogenesis of ''(M. tb)'' <ref name="molecular studies"/>.<br />
<br />
== Relevance of key mutational studies to the understanding and development of new inhibitors for FadD13 ==<br />
<br />
<ref name="residue paper"/><br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393456Sandbox Reserved 10662015-04-09T01:56:49Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane.<ref name="Our Paper"/> This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
FadD13 has be identified as key to the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interactions of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 3).<ref name="Our Paper"/> <br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
Mutational studies showed that high conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic aicds, which are known to play a crucial role in pathogenesis of ''(M. tb)'' <ref name="molecular studies"/>.<br />
<br />
== Relevance of key mutational studies to the understanding and development of new inhibitors for FadD13 ==<br />
<br />
<ref name="residue paper"/><br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393453Sandbox Reserved 10662015-04-09T01:51:32Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane.<ref name="Our Paper"/> This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
FadD13 has be identified as key to the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref> The FadD13 enzyme is the last gene of the ''mymA'' operon. <ref name="residue paper"/><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 represents the first Fatty Acyl-CoA Synthetase of its kind to display biphasic kinetics.<ref name="residue paper"/> FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and subsequently releases a pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2). These activated fatty acyl-CoA thioesters have then been demonstrated to be important for the synthesis of triacyglycerols and phospholipids in the membrane of ''Mycobacterium tuberculosis''. <ref name="residue paper"/><br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14 (Figure 3).<ref name="Our Paper"/> <br />
[[Image:Hydrophobic tunnel 2.jpg|300 px|left|thumb|Figure 4: Pmyol depiction of hydrophobic tunnel.]]<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
Mutational studies showed that high conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic aicds, which are known to play a crucial role in pathogenesis of ''(M. tb)'' <ref name="molecular studies"/>.<br />
<br />
== Relevance of key mutational studies to the understanding and development of new inhibitors for FadD13 ==<br />
<br />
<ref name="residue paper"/><br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=File:Hydrophobic_tunnel_2.jpg&diff=2393448File:Hydrophobic tunnel 2.jpg2015-04-09T01:47:57Z<p>Joseph Thomas: </p>
<hr />
<div></div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393424Sandbox Reserved 10662015-04-09T01:24:52Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Figure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (Figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
Mutational studies showed that high conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic aicds, which are known to play a crucial role in pathogenesis of ''(M. tb)'' <ref name="molecular studies"/>.<br />
<br />
== Relevance of key mutational studies to the understanding and development of new inhibitors for FadD13 ==<br />
<br />
<ref name="residue paper"/><br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393421Sandbox Reserved 10662015-04-09T01:24:02Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
Mutational studies showed that high conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic aicds, which are known to play a crucial role in pathogenesis of ''(M. tb)'' <ref name="molecular studies"/>.<br />
<br />
== Relevance of key mutational studies to the understanding and development of new inhibitors for FadD13 ==<br />
<br />
<ref name="residue paper"/><br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393420Sandbox Reserved 10662015-04-09T01:22:54Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<scene name='69/694233/Lys_487/2'>Lys 487</scene> results in a 95% loss of function of FadD13. <ref name="residue paper">PMID: 20027301</ref><br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
Mutational studies showed that high conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections along with the increase in multi-drug resistance strains of ''(M. tb)'' <ref name="molecular studies">PMID: 20454815</ref>. Most of the drug resistance has evolved due to the intensive nature of the treatment for tuberculosis, which often goes incomplete thus resulting in drug resistant strains; therefore, the importance in identifying characteristics and residues to be exploited for new drug targets is pivotal <ref name="molecular studies"/>.<br />
<br />
The cell wall of ''(M. tb)'' is known to be composed and synthesized from a distinct variety of lipids, most notably mycolic aicds, which are known to play a crucial role in pathogenesis of ''(M. tb)'' <ref name="molecular studies"/>.<br />
<br />
== Relevance of key mutational studies to the understanding and development of new inhibitors for FadD13 ==<br />
<br />
<ref name="residue paper"/><br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1065&diff=2393417Sandbox Reserved 10652015-04-09T01:16:38Z<p>Joseph Thomas: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
<br />
==Your Heading Here (maybe something like 'Structure')==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 1).<br />
<br />
=active site (to be copied over)=<br />
<br />
Mutational studies showed that high conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Additionally, Serine 404 was hypothesized to be involved in the binding of Coenzyme A which may only occur once this region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
<br />
<br />
== Function ==<br />
<br />
<br />
This is the <scene name='69/694232/Arginine_rich_lid_loop/1'>Arginie-rich lid loop</scene>.<ref name="OUR PAPER">PMID: 22560731</ref><br />
<br />
This is the <scene name='69/694232/Linker_section/2'>linker</scene>.<ref name="OUR PAPER"/><br />
<br />
FadD13 has three different <scene name='69/694232/Domains/2'>regions</scene>: The N-terminal region (1-395) is in blue, the C-terminal region (402-403) is in red, and the six amino acid linker is in tan (citation for original paper). <br />
<br />
The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases (Citation for original paper). <br />
<br />
citation 1 <ref name="Our Paper">PMID: 22560731</ref><br />
<ref name="OUR PAPER"/><br />
<br />
citation 2 <ref name="JT">PMID: 20454815</ref><br />
<ref name="JT"/><br />
<br />
Citation 3 <ref name="SM">PMID: 12164478</ref><br />
<ref name="SM"/><br />
<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1065&diff=2393414Sandbox Reserved 10652015-04-09T01:15:18Z<p>Joseph Thomas: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
<br />
==Your Heading Here (maybe something like 'Structure')==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 1).<br />
<br />
=active site (to be copied over)=<br />
<br />
A high conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Other mutation studies, found that Serine 404 was involved in the binding of Coenzyme A which may only occur once the region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
<br />
<br />
== Function ==<br />
<br />
<br />
This is the <scene name='69/694232/Arginine_rich_lid_loop/1'>Arginie-rich lid loop</scene>.<ref name="OUR PAPER">PMID: 22560731</ref><br />
<br />
This is the <scene name='69/694232/Linker_section/2'>linker</scene>.<ref name="OUR PAPER"/><br />
<br />
FadD13 has three different <scene name='69/694232/Domains/2'>regions</scene>: The N-terminal region (1-395) is in blue, the C-terminal region (402-403) is in red, and the six amino acid linker is in tan (citation for original paper). <br />
<br />
The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases (Citation for original paper). <br />
<br />
citation 1 <ref name="Our Paper">PMID: 22560731</ref><br />
<ref name="OUR PAPER"/><br />
<br />
citation 2 <ref name="JT">PMID: 20454815</ref><br />
<ref name="JT"/><br />
<br />
Citation 3 <ref name="SM">PMID: 12164478</ref><br />
<ref name="SM"/><br />
<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1065&diff=2393412Sandbox Reserved 10652015-04-09T01:13:59Z<p>Joseph Thomas: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
<br />
==Your Heading Here (maybe something like 'Structure')==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 1).<br />
<br />
=active site (to be copied over)=<br />
<br />
A high conserved residue in the C-terminal region,<scene name='69/694233/Lys_487/2'>Lys 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Other mutation studies, found that Serine 404 was involved in the binding of Coenzyme A which may only occur once the region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/><br />
<br />
<br />
<br />
<br />
== Function ==<br />
<br />
<br />
This is the <scene name='69/694232/Arginine_rich_lid_loop/1'>Arginie-rich lid loop</scene>.<ref name="OUR PAPER">PMID: 22560731</ref><br />
<br />
This is the <scene name='69/694232/Linker_section/2'>linker</scene>.<ref name="OUR PAPER"/><br />
<br />
FadD13 has three different <scene name='69/694232/Domains/2'>regions</scene>: The N-terminal region (1-395) is in blue, the C-terminal region (402-403) is in red, and the six amino acid linker is in tan (citation for original paper). <br />
<br />
The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases (Citation for original paper). <br />
<br />
citation 1 <ref name="Our Paper">PMID: 22560731</ref><br />
<ref name="OUR PAPER"/><br />
<br />
citation 2 <ref name="JT">PMID: 20454815</ref><br />
<ref name="JT"/><br />
<br />
Citation 3 <ref name="SM">PMID: 12164478</ref><br />
<ref name="SM"/><br />
<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393406Sandbox Reserved 10662015-04-09T01:00:57Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<scene name='69/694233/Lys_487/2'>Lys 487</scene> results in a 95% loss of function of FadD13. <ref name="residue paper">PMID: 20027301</ref><br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' ''(M.tb)'' is the causative agent involved in the disease '''tuberculosis'''. Tuberculosis is a growing global health concern that has been intensified due to the increase in HIV infections and multi-drug resistance strains of ''(M. tb)''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393404Sandbox Reserved 10662015-04-09T00:59:25Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<scene name='69/694233/Lys_487/2'>Lys 487</scene> results in a 95% loss of function of FadD13. <ref name="residue paper">PMID: 2793005</ref><br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393403Sandbox Reserved 10662015-04-09T00:58:52Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<scene name='69/694233/Lys_487/2'>Lys 487</scene> results in a 95% loss of function of FadD13. <ref name="residue paper">PMCID: PMC2793005</ref><br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393402Sandbox Reserved 10662015-04-09T00:58:20Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<scene name='69/694233/Lys_487/2'>Lys 487</scene> results in a 95% loss of function of FadD13. <ref name="residue paper">PMCID: PMC2793005ref><br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393400Sandbox Reserved 10662015-04-09T00:57:42Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<scene name='69/694233/Lys_487/2'>Lys 487</scene> results in a 95% loss of function of FadD13. <ref name="residue paper">PMCID: PMC2793005/ref><br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393399Sandbox Reserved 10662015-04-09T00:56:26Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<scene name='69/694233/Lys_487/2'>Lys 487</scene> results in a 95% loss of function of FadD13. <ref name="residue paper">PMID: PMC2793005</ref><br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2393398Sandbox Reserved 10662015-04-09T00:55:30Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
<scene name='69/694233/Lys_487/2'>Lys 487</scene> results in a 95% loss of function of FadD13. <ref name="Our Paper">PMID: PMC2793005</ref><br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
<br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391571Sandbox Reserved 10662015-04-07T00:07:08Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the [http://en.wikipedia.org/wiki/Acyl-CoA acyl CoA] product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[http://en.wikipedia.org/wiki/Acyl-CoA Acyl CoA] Wikipedia Page<br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391570Sandbox Reserved 10662015-04-07T00:05:27Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure 3: Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391569Sandbox Reserved 10662015-04-07T00:04:58Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (Fiigure 3) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391568Sandbox Reserved 10662015-04-07T00:03:15Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/N_terminal_domain/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/2'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694233/Linker_section/2'>linker</scene> represented in dark blue (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391567Sandbox Reserved 10662015-04-06T23:51:35Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|425 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|425 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694232/Linker_section/2'>linker</scene> (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391566Sandbox Reserved 10662015-04-06T23:50:03Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
[[Image:FadD13 edited image.jpg|400 px|left|thumb|Figure 1: Mechanism for the activation of fatty acids (C24-C26) by FadD13. The N terminal domain (pink) is embedded in the membrane with the arginine rich lid-loop (dark blue), while the flexile linker (black) connects the C terminal domain (green) to the rest of the enzyme. Activation requires the binding of ATP (blue) which induces structural changes that promote the binding of the fatty acid chain. Formation of an acyl-adenylate intermediate induces a 140° rotation of the C terminal domain and the binding of CoA (orange). ]]<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure 2: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 2).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
=Structure =<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694232/Linker_section/2'>linker</scene> (residues 396-401).<ref name="Our Paper"/> Each region plays an important role in the activation of fatty acids. The large N-terminal domain has the most structural features, but it is ultimately the flexible linker that allows movement of the C-terminal domain to from the fully functioning active site (Figure 1).<br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results revealed that the peripheral FadD13 is attached to the membrane via electrostatic and hydrophobic regions located on the top portion of the N-terminal region (figure 3).<ref name="Our Paper"/> Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.This area on the top portion of the enzyme is also crucial in the association with the membrane as the positively charged arginine residues are attracted to the negative charge on the phospholipid heads.<ref name="Our Paper"/><br />
<br />
== Hydrophobic Tunnel ==<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases. <ref name="Our Paper"/><br />
<br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391071Sandbox Reserved 10662015-04-03T18:38:02Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure 1: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 1).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
<br />
= Structure =<br />
== General overview ==<br />
<br />
This is the <scene name='69/698726/Overall_structure_cartoon/1'>overall structure of FadD13</scene><br />
<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible <scene name='69/694232/Linker_section/2'>linker</scene> (residues 396-401).<ref name="Our Paper"/><br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results from (Paper) revealed that the peripheral FadD13 attached to the membrane via positively charges interacting with the negatively charged cell membrane (image) located on the top portion of the N-terminal region. Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.<br />
<br />
== Hydrophobic Tunnel ==<br />
<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases (Citation for original paper). <br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1065&diff=2391068Sandbox Reserved 10652015-04-03T18:34:00Z<p>Joseph Thomas: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
<br />
==Your Heading Here (maybe something like 'Structure')==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 1).<br />
<br />
<br />
<br />
== Function ==<br />
<br />
<br />
This is the <scene name='69/694232/Arginine_rich_lid_loop/1'>Arginie-rich lid loop</scene>.<ref name="OUR PAPER">PMID: 22560731</ref><br />
<br />
This is the <scene name='69/694232/Linker_section/2'>linker</scene>.<ref name="OUR PAPER"/><br />
<br />
FadD13 has three different <scene name='69/694232/Domains/2'>regions</scene>: The N-terminal region (1-395) is in blue, the C-terminal region (402-403) is in red, and the six amino acid linker is in tan (citation for original paper). <br />
<br />
The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases (Citation for original paper). <br />
<br />
citation 1 <ref name="Our Paper">PMID: 22560731</ref><br />
<ref name="OUR PAPER"/><br />
<br />
citation 2 <ref name="JT">PMID: 20454815</ref><br />
<ref name="JT"/><br />
<br />
Citation 3 <ref name="SM">PMID: 12164478</ref><br />
<ref name="SM"/><br />
<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391067Sandbox Reserved 10662015-04-03T18:31:18Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure 1: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 1).<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein with a hydrophobic tunnel. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
<br />
= Structure =<br />
== General overview ==<br />
<br />
This is the <scene name='69/698726/Overall_structure_cartoon/1'>overall structure of FadD13</scene><br />
<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible linker (residues 396-401).<ref name="Our Paper"/><br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results from (Paper) revealed that the peripheral FadD13 attached to the membrane via positively charges interacting with the negatively charged cell membrane (image) located on the top portion of the N-terminal region. Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.<br />
<br />
== Hydrophobic Tunnel ==<br />
<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The <br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391061Sandbox Reserved 10662015-04-03T18:23:19Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure 1: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
<br />
= Structure =<br />
== General overview ==<br />
<br />
This is the <scene name='69/698726/Overall_structure_cartoon/1'>overall structure of FadD13</scene><br />
<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible linker (residues 396-401).<ref name="Our Paper"/><br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results from (Paper) revealed that the peripheral FadD13 attached to the membrane via positively charges interacting with the negatively charged cell membrane (image) located on the top portion of the N-terminal region. Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.<br />
<br />
== Hydrophobic Tunnel ==<br />
<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The <br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391058Sandbox Reserved 10662015-04-03T18:22:16Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure 1: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
<br />
= Structure =<br />
== General overview ==<br />
<br />
This is the <scene name='69/698726/Overall_structure_cartoon/1'>overall structure of FadD13</scene><br />
<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible linker (residues 396-401).<ref name="Our Paper"/><br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results from (Paper) revealed that the peripheral FadD13 attached to the membrane via positively charges interacting with the negatively charged cell membrane (image) located on the top portion of the N-terminal region. Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.<br />
<br />
== Hydrophobic Tunnel ==<br />
<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The <br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[http://en.wikipedia.org/wiki/Coenzyme_A Coenzyme A] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391053Sandbox Reserved 10662015-04-03T18:19:52Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's activation and transport of fatty acids of length C24-C26 through the two step addition of [https://en.wikipedia.org/wiki/Acyl-CoA Acyl-CoA](Figure 1).<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure 1: Representation of the two-step reaction catalyzed by FadD13]]<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
<br />
= Structure =<br />
== General overview ==<br />
<br />
This is the <scene name='69/698726/Overall_structure_cartoon/1'>overall structure of FadD13</scene><br />
<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible linker (residues 396-401).<ref name="Our Paper"/><br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results from (Paper) revealed that the peripheral FadD13 attached to the membrane via positively charges interacting with the negatively charged cell membrane (image) located on the top portion of the N-terminal region. Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.<br />
<br />
== Hydrophobic Tunnel ==<br />
<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The <br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Acyl-CoA Acyl-CoA] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391043Sandbox Reserved 10662015-04-03T18:13:20Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's transport of fatty acids of length C24-C26.<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure Legend]]<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
<br />
= Structure =<br />
== General overview ==<br />
<br />
This is the <scene name='69/698726/Overall_structure_cartoon/1'>overall structure of FadD13</scene><br />
<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible linker (residues 396-401).<ref name="Our Paper"/><br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results from (Paper) revealed that the peripheral FadD13 attached to the membrane via positively charges interacting with the negatively charged cell membrane (image) located on the top portion of the N-terminal region. Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.<br />
<br />
== Hydrophobic Tunnel ==<br />
<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The <br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Acyl-CoA Acyl-CoA] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391042Sandbox Reserved 10662015-04-03T18:12:19Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's transport of fatty acids of length C24-C26.<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure Legend]]<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
<br />
= Structure =<br />
== General overview ==<br />
<br />
This is the <scene name='69/698726/Overall_structure_cartoon/1'>overall structure of FadD13</scene><br />
<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible linker (residues 396-401).<ref name="Our Paper"/><br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results from (Paper) revealed that the peripheral FadD13 attached to the membrane via positively charges interacting with the negatively charged cell membrane (image) located on the top portion of the N-terminal region. Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.<br />
<br />
== Hydrophobic Tunnel ==<br />
<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The <br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
__NOTOC__<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Acyl-CoA Acyl-CoA] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=User:Joseph_Thomas&diff=2391024User:Joseph Thomas2015-04-03T17:52:17Z<p>Joseph Thomas: </p>
<hr />
<div>*[[User:Joseph Thomas/Sandbox 1]]<br />
*[[User:Joseph Thomas/Sandbox 2]]<br />
* Full Real Name:<br />
Joseph Thomas<br />
* Position:<br />
Student<br />
* Institution (NO ABBREVIATIONS):<br />
Butler University <br />
* City, State/Province, Country:<br />
Indianapolis, Indiana, United States of America<br />
* Field of Expertise or Study:<br />
Chemistry</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391018Sandbox Reserved 10662015-04-03T17:44:25Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's transport of fatty acids of length C24-C26.<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure Legend]]<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
<br />
= Structure =<br />
== General overview ==<br />
<br />
This is the <scene name='69/698726/Overall_structure_cartoon/1'>overall structure of FadD13</scene><br />
<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible linker (residues 396-401).<ref name="Our Paper"/><br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results from (Paper) revealed that the peripheral FadD13 attached to the membrane via positively charges interacting with the negatively charged cell membrane (image) located on the top portion of the N-terminal region. Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.<br />
<br />
== Hydrophobic Tunnel ==<br />
<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The <br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Acyl-CoA Acyl-CoA] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391015Sandbox Reserved 10662015-04-03T17:42:44Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
==Your Heading Here (maybe something like 'Structure')==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's transport of fatty acids of length C24-C26.<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents.<ref name="JT">PMID: 20454815</ref><br />
<br />
= Mechanism =<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure Legend]]<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
<br />
= Structure =<br />
== General overview ==<br />
<br />
This is the <scene name='69/698726/Overall_structure_cartoon/1'>overall structure of FadD13</scene><br />
<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible linker (residues 396-401).<ref name="Our Paper"/><br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results from (Paper) revealed that the peripheral FadD13 attached to the membrane via positively charges interacting with the negatively charged cell membrane (image) located on the top portion of the N-terminal region. Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.<br />
<br />
== Hydrophobic Tunnel ==<br />
<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The <br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Acyl-CoA Acyl-CoA] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391014Sandbox Reserved 10662015-04-03T17:40:45Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
<br />
==Your Heading Here (maybe something like 'Structure')==<br />
<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
<br />
<br />
= Introduction =<br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's transport of fatty acids of length C24-C26.<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''], the etiological agent of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis], and has emerged as possible target for novel therapeutic agents. <br />
<br />
= Mechanism =<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure Legend]]<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
<br />
= Structure =<br />
== General overview ==<br />
<br />
This is the <scene name='69/698726/Overall_structure_cartoon/1'>overall structure of FadD13</scene><br />
<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible linker (residues 396-401).<ref name="Our Paper"/><br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results from (Paper) revealed that the peripheral FadD13 attached to the membrane via positively charges interacting with the negatively charged cell membrane (image) located on the top portion of the N-terminal region. Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.<br />
<br />
== Hydrophobic Tunnel ==<br />
<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The <br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Acyl-CoA Acyl-CoA] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomashttps://proteopedia.org/index.php?title=Sandbox_Reserved_1066&diff=2391010Sandbox Reserved 10662015-04-03T17:37:02Z<p>Joseph Thomas: </p>
<hr />
<div><blockquote></blockquote>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'><br />
This is a default text for your page '''StephanieShoults/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
= Introduction =<br />
<br />
== ''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase ==<br />
''Mycobacterium tuberculosis'' very-long-chain fatty acyl-CoA synthetase, also known as FadD13, is unique within its class in regards to its ability to house lipid substrates longer than itself. Most FadD class proteins exist as integral membrane proteins involved in lipid transport into the cell. FadD13 is unique structurally in that it exists as a peripheral protein on the inside of the cell membrane. This feature is key in the mechanistic basis for FadD13's transport of fatty acids of length C24-C26.<ref name="Our Paper">PMID: 22560731</ref><br />
<br />
FadD13 may be important in the virulence of [https://en.wikipedia.org/wiki/Tuberculosis tuberculosis] and has emerged as possible target for therapeutic agents. <br />
= Mechanism =<br />
<br />
== General mechanism for the activation of fatty acids ==<br />
<br />
[[Image:acyl coa synthetase.jpg|400 px|left|thumb|Figure Legend]]<br />
<br />
== Structural basis for housing lipid substrates longer than the enzyme ==<br />
<br />
The ability for FadD13 to transport and activate fatty acids of the maximum tested length C26, lies in it being a peripheral membrane protein. FadD13 is attached to the membrane via electrostatic interactions in the N-terminal domain. Of importance in the region is the arginine rich lid-loop which serves to block the transport of fatty acids into the enzyme. Once the lid-loop is opened, fatty acids may be pulled from the membrane into a hydrophobic tunnel, which is the main structural component by which fatty acids are transported from the membrane into the cell. Negatively charged residues at the active site of FadD13 are the driving factor in the attraction of the fatty acid from the membrane through the hydrophobic tunnel of the enzyme.<br />
<br />
<br />
= Structure =<br />
== General overview ==<br />
<br />
This is the <scene name='69/698726/Overall_structure_cartoon/1'>overall structure of FadD13</scene><br />
<br />
FadD13 is composed of 503 amino acid residues divided into three main regions: The <scene name='69/694233/Domains/1'>N-terminal domain</scene> (residues 1-395) and <scene name='69/694233/C-terminal_domain/1'>C-terminal domain</scene> (residues 402-503) which are connected via a flexible linker (residues 396-401).<ref name="Our Paper"/><br />
<br />
<br />
<br />
== Electrostatics ==<br />
[[Image:electrostatics fadD13.png|300 px|left|thumb|Figure Legend. Pmyol depiction of electrostatic interaction of FadD13.]]<br />
The electrostatics of FadD13 as seen in (figure...) illustrate the hydrophobic and positively charged regions that compose this protein. Experimental results from (Paper) revealed that the peripheral FadD13 attached to the membrane via positively charges interacting with the negatively charged cell membrane (image) located on the top portion of the N-terminal region. Of key importance in this N-terminal domain region attached to the membrane is an area of notable arginine rich residues, known as the arginine rich lid-loop.<br />
<br />
== Arginine Rich Lid-loop ==<br />
<br />
The <scene name='69/694233/Arginine_rich_lid_loop/1'>arginine rich lid loop</scene> functions to block entry of fatty acids into the hydrophobic tunnel of FadD13.<br />
<br />
== Hydrophobic Tunnel ==<br />
<br />
The hydrophobic tunnel of FadD13 is essential to the transport and accommodation of very long fatty acids from the membrane into the cell. This tunnel runs through the middle of FadD13 from the arginine rich lid loop to the ATP binding site and is situated between the and alpha helices α8-α9 and parallel beta sheet β9- β14.<ref name="Our Paper"/><br />
<br />
== Active Site ==<br />
<br />
The active site on FadD13 is composed of two conserved regions, one of which serves as the binding site for ATP and the other for CoA. The <br />
= Disease =<br />
''Mycobacterium tuberculosis'' is the causative agent involved in the disease '''tuberculosis'''.<br />
<br />
== Relevance ==<br />
<br />
== Inhibitors ==<br />
<br />
== Future Research ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/><br />
<br />
==Similar Proteopedia Pages==<br />
[http://www.proteopedia.org/wiki/index.php/Thioesterase Thioesterase] Do we have anything like this? <br />
<br />
<br />
<br />
==External Resources==<br />
<br />
[https://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis''] Wikipedia page<br />
<br />
[https://en.wikipedia.org/wiki/Acyl-CoA Acyl-CoA] Wikipedia page <br />
<br />
[https://en.wikipedia.org/wiki/Mycolic_acid Mycolic Acid] Wikipedia page</div>Joseph Thomas