Proteopedia - User contributions [en]

Methionine synthase

2022-05-02T15:27:37Z

Kia Yang:

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

== Function ==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 displaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM<ref>DOI:10.1073/pnas.1133218100</ref>.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
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As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|300px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

DMB, in the lower ligand of the <scene name='90/907471/Bindingdomain2/2'>B12 binding domain</scene> is displaced from the Cobalt by a Histidine residue to be 'uncapped' to form Me-Cob(III)alamin<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref>.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
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=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/2'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-02T14:37:52Z

Kia Yang:

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

== Function ==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM<ref>DOI:10.1073/pnas.1133218100</ref>.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
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<item>
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</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|300px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

DMB, in the lower ligand of the <scene name='90/907471/Bindingdomain2/2'>B12 binding domain</scene> is displaced from the Cobalt by a Histidine residue to be 'uncapped' to form Me-Cob(III)alamin<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref>.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
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=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/2'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-02T14:37:01Z

Kia Yang:

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

== Function ==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM<ref>DOI:10.1073/pnas.1133218100</ref>.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
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</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|300px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

DMB, in the lower ligand of the <scene name='90/907471/Bindingdomain2/2'>B12 binding domain</scene> is displaced from the Cobalt by a Histidine residue to be 'uncapped' to form Me-Cob(III)alamin<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref>.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
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=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1/2'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-02T13:13:59Z

Kia Yang:

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

== Function ==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM<ref>DOI:10.1073/pnas.1133218100</ref>.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
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</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|300px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

DMB, in the lower ligand of the <scene name='90/907471/Bindingdomain2/2'>B12 binding domain</scene> is displaced from the Cobalt by a Histidine residue to be 'uncapped' to form Me-Cob(III)alamin<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref>.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T16:55:19Z

Kia Yang:

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

===Function===

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

=== Oxidation States of Cobalamin ===

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM<ref>DOI:10.1073/pnas.1133218100</ref>.

=== Relevance ===

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

=== Structural highlights ===

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

== Domain organization ==

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Cobalamin binding ==

[[Image:cob_1_alamin.jpeg|300px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

DMB, in the lower ligand of the <scene name='90/907471/Bindingdomain2/2'>B12 binding domain</scene> is displaced from the Cobalt by a Histidine residue to be 'uncapped' to form Me-Cob(III)alamin<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref>.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

== Cobalamin activation ==

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

</StructureSection>

=== Acknowledgements ===

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

=== References ===

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T16:48:24Z

Kia Yang:

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

===Function===

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

=== Oxidation States of Cobalamin ===

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM<ref>DOI:10.1073/pnas.1133218100</ref>.

=== Relevance ===

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

=== Structural highlights ===

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

== Domain organization ==

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Cobalamin binding ==

[[Image:cob_1_alamin.jpeg|300px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

DMB, in the lower ligand of the <scene name='90/907471/Bindingdomain2/1'>B12 binding domain</scene> is displaced from the Cobalt by a Histidine residue to be 'uncapped' to form Me-Cob(III)alamin<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref>.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

== Cobalamin activation ==

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

</StructureSection>

=== Acknowledgements ===

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

=== References ===

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T16:48:00Z

Kia Yang:

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

===Function===

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

=== Oxidation States of Cobalamin ===

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM<ref>DOI:10.1073/pnas.1133218100</ref>.

=== Relevance ===

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

== Domain organization ==

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Cobalamin binding ==

[[Image:cob_1_alamin.jpeg|300px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

DMB, in the lower ligand of the <scene name='90/907471/Bindingdomain2/1'>B12 binding domain</scene> is displaced from the Cobalt by a Histidine residue to be 'uncapped' to form Me-Cob(III)alamin<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref>.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

== Cobalamin activation ==

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

</StructureSection>

=== Acknowledgements ===

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

=== References ===

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T16:47:48Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

===Function===

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

=== Oxidation States of Cobalamin ===

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM<ref>DOI:10.1073/pnas.1133218100</ref>.

=== Relevance ===

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

== Domain organization ==

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Cobalamin binding ==

[[Image:cob_1_alamin.jpeg|300px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

DMB, in the lower ligand of the <scene name='90/907471/Bindingdomain2/1'>B12 binding domain</scene> is displaced from the Cobalt by a Histidine residue to be 'uncapped' to form Me-Cob(III)alamin<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref>.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

== Cobalamin activation ==

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

</StructureSection>

=== Acknowledgements ===

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

=== References ===

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T16:47:36Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

===Function===

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

=== Oxidation States of Cobalamin ===

[[Image: MS_cycle.gif|400px]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM<ref>DOI:10.1073/pnas.1133218100</ref>.

=== Relevance ===

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

== Domain organization ==

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Cobalamin binding ==

[[Image:cob_1_alamin.jpeg|300px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

DMB, in the lower ligand of the <scene name='90/907471/Bindingdomain2/1'>B12 binding domain</scene> is displaced from the Cobalt by a Histidine residue to be 'uncapped' to form Me-Cob(III)alamin<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref>.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

== Cobalamin activation ==

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

</StructureSection>

=== Acknowledgements ===

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

=== References ===

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T16:46:08Z

Kia Yang:

Methionine synthase

2022-05-01T16:45:01Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

===Function===

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

=== Oxidation States of Cobalamin ===

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM<ref>DOI:10.1073/pnas.1133218100</ref>.

=== Relevance ===

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

== Domain organization ==

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Cobalamin binding ==

[[Image:cob_1_alamin.jpeg|300px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

DMB, in the lower ligand of the <scene name='90/907471/Bindingdomain2/1'>B12 binding domain</scene> is displaced from the Cobalt by a Histidine residue to be 'uncapped' to form Me-Cob(III)alamin<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref>.

== Cobalamin activation ==

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

=== Acknowledgements ===

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

=== References ===

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T16:42:44Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

===Function===

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

=== Oxidation States of Cobalamin ===

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

=== Relevance ===

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

== Domain organization ==

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Cobalamin binding ==

[[Image:cob_1_alamin.jpeg|300px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

DMB, in the lower ligand of the <scene name='90/907471/Bindingdomain2/1'>B12 binding domain</scene> is displaced from the Cobalt by a Histidine residue to be 'uncapped' to form Me-Cob(III)alamin.

== Cobalamin activation ==

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

=== Acknowledgements ===

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

=== References ===

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T16:40:14Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

===Function===

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

=== Oxidation States of Cobalamin ===

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

=== Relevance ===

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

== Domain organization ==

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Cobalamin binding ==

[[Image:cob_1_alamin.jpeg|250px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

The lower ligand of the <scene name='90/907471/Bindingdomain2/1'>B12 binding domain</scene> is where DMB is displaced from the Cobalt by a Histidine residue to form Me-Cob(III)alamin.

== Cobalamin activation ==

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

=== Acknowledgements ===

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

=== References ===

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T16:39:35Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine and tetrahydrofolate (THF). Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

===Function===

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as THF, a product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

=== Oxidation States of Cobalamin ===

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

=== Relevance ===

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

== Domain organization ==

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Cobalamin binding ==

[[Image:cob_1_alamin.jpeg|500px]]

The Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

The lower ligand of the<scene name='90/907471/Bindingdomain2/1'>B12 binding domain</scene> is where DMB is displaced from the Cobalt by a Histidine residue to form Me-Cob(III)alamin.

== Cobalamin activation ==

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

=== Acknowledgements ===

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

=== References ===

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:47:42Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

===Function===

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

=== Oxidation States of Cobalamin ===

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

=== Relevance ===

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>

== Domain organization ==

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Cobalamin binding ==

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

== Cobalamin activation ==

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
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<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

=== Acknowledgements ===

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

=== References ===

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:41:35Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

===Function===

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

=== Oxidation States of Cobalamin ===

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

=== Relevance ===

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/2'>

== Domain organization ==

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Cobalamin binding ==

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

== Cobalamin activation ==

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
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<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

=== Acknowledgements ===

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

=== References ===

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:40:05Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/2'>

=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

<scene name='90/907471/Superposition_1/2'>Text To Be Displayed</scene>

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
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<text>animate</text>
<checked>false</checked>
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</jmol>

</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:36:25Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='1k7y' size='400' side='right' scene='90/907471/Superposition_1/2' scene='MS'>

=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

<scene name='90/907471/Superposition_1/2'>Text To Be Displayed</scene>

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
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<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:29:47Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='1k7y' size='400' side='right' caption='' scene='caption here'>

=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

<scene name='90/907471/Superposition_1/2'>Text To Be Displayed</scene>

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
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<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
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<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
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<text>animate</text>
<checked>false</checked>
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</jmolRadioGroup>
</jmol>

</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:26:25Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='<scene name='90/907471/Superposition_1/2'>initial scene</scene>' size='310' side='right' caption='N-terminal containing catalytic cycle with two domains: 5-me THF and Hcy. C-terminal containing reactivation cycle with two domains: Cobalamin and SAM' (PBD ID: 1k7y)' scene=''>

=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

<scene name='90/907471/Superposition_1/2'>Text To Be Displayed</scene>

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
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<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
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</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:24:56Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<scene name='90/907471/Superposition_1/2'>Text To Be Displayed</scene>

Load <StructureSection load='<scene name='90/907471/Superposition_1/2'>initial scene</scene>' size='310' side='right' caption='N-terminal containing catalytic cycle with two domains: 5-me THF and Hcy. C-terminal containing reactivation cycle with two domains: Cobalamin and SAM' (PBD ID: 1k7y)' scene=''>

=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:22:32Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]<scene name='90/907471/Superposition_1/2'>Text To Be Displayed</scene>

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

Load <StructureSection load='<scene name='90/907471/Superposition_1/2'>initial scene</scene>' size='310' side='right' caption='N-terminal containing catalytic cycle with two domains: 5-me THF and Hcy. C-terminal containing reactivation cycle with two domains: Cobalamin and SAM' (PBD ID: 1k7y)' scene=''>

=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:22:02Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]<scene name='90/907471/Superposition_1/2'>Text To Be Displayed</scene>

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==

<StructureSection load='<scene name='90/907471/Superposition_1/2'>Text To Be Displayed</scene>' size='310' side='right' caption='N-terminal containing catalytic cycle with two domains: 5-me THF and Hcy. C-terminal containing reactivation cycle with two domains: Cobalamin and SAM' (PBD ID: 1k7y)' scene=''>

=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
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<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
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</jmol>

</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:21:28Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]<scene name='90/907471/Superposition_1/2'>Text To Be Displayed</scene>

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==
<StructureSection load='<scene name='90/907471/Superposition_1/2'>1k7y</scene>' size='310' side='right' caption='C-terminal fragment of MS (PDB ID: 1k7y)' scene=''>
<scene name='90/907471/Superposition_1/2'>Text To Be Displayed</scene>' size='310' side='right' caption='N-terminal containing catalytic cycle with two domains: 5-me THF and Hcy. C-terminal containing reactivation cycle with two domains: Cobalamin and SAM' (PBD ID: 1k7y)' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
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</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:12:34Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==
<StructureSection load='1k7y' size='310' side='right' caption='C-terminal fragment of MS (PDB ID: 1k7y)' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
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<text>with activation domain</text>
<checked>false</checked>
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<text>animate</text>
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</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-05-01T15:11:23Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: MS_cycle.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink. (PDB ID: 1BMT)' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

Every 2000 or so cycles, cobalamin needs to be <scene name='90/907471/B12_activation_w_sah/1'>reactivated</scene> through methylation by S-adenosyl methionine (SAM). To determine the structure of the reactivation conformation, the mutant H759G was used. This mutation maximises the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
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<text>capped</text>
<checked>true</checked>
</item>
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<text>with activation domain</text>
<checked>false</checked>
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</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

File:MS cycle.gif

2022-05-01T15:10:57Z

Kia Yang: updated gif for MS cycles

updated gif for MS cycles

Methionine synthase

2022-04-27T15:05:30Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: Overall_methionine.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink. (PDB ID: 1BMT)' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determine.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
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</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their enthusiasm and assistance on creation of 3D structural images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing helpful suggestions for improvement.

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-27T15:01:43Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: Overall_methionine.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink. (PDB ID: 1BMT)' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determine.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
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As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring as seen in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> comes in and out of the B12 domain as the 5th ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the Cobalamin moves a bit out of the reach of the Histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
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<text>capped</text>
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<item>
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</StructureSection>

== Acknowledgements ==

Many thanks to Dr. Theis, Anna, Mike, and Shaylie for their assistance on creation of 3D images of the B12 domain for MS.

Also thanks to Dr. Drennan for taking the time to review the page and providing very

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-26T23:41:45Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: Overall_methionine.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink. (PDB ID: 1BMT)' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determine.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
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<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
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</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring very similar to what we see in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>, we can see where the DMB ligand exists. During its confirmation change, DMB will move away from the Corrin ring and replaced by His 757.

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
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<text>capped</text>
<checked>true</checked>
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<text>with activation domain</text>
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</StructureSection>

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine adenosyltransferase

2022-04-25T15:09:31Z

Kia Yang:

[[Methionine adenosyltransferase]] (MAT) or S-adenosylmethionine synthetase (SAM synthetase) synthesizes S-adenosylmethionine (SAM or AdoMet) from the substrates adenosine triphosphate (ATP) and methionine. ATP isn’t used only as a source of energy like it is in other reactions but gets a methionine added onto the 5' carbon while the three phosphate groups are broken down and released from the active site. This enzyme is conserved and found in many organisms, so it is essential for life. Importantly, the production of SAM by MAT provides methyl for methylation of nucleic acids, allowing for epigenetic modification. Problems with this enzyme have been shown to cause diseases including various cancers.

== Relevance ==
The product of this enzymatic reaction, SAM, is the universal methyl donor of metabolism. DNA methyltransferases can transfer a methyl group from SAM to the 5th carbon of cytosine residues <ref>DOI:10.1038/npp.2012.112</ref>. In this way, MAT is indirectly important for regulation of gene expression by providing methyl through SAM. SAM is also involved in N-methylation, O-methylation and C-methylation, yielding S-adenosyl homocysteine as a product that gets recycled by the [[one-carbon metabolism]]. Radical SAM enzymes break down SAM into an adenosyl radical and methionine, enabling a host of otherwise difficult to achieve reactions, e.g. in molybdenum cofactors biosynthesis<ref>DOI:10.1073/pnas.0404624101</ref>. Accumulation of S-adenosyl homocysteine (or homocysteine itself) indicates an imbalance in supply and demand for SAM in the organism. Methionine metabolism impairment in liver diseases is related in alteration in MAT<ref>PMID:7741002</ref>.

== Function and reaction mechanism ==
'''S-adenosylmethionine synthetase''' or '''S-adenosylmethionine synthase''' or '''S-adenosylmethionine transferase''' or '''methionine adenosyltransferase''' (MAT) catalyzes the conversion of methionine and ATP to S-adenosylmethionine (AdoMet), pyrophosphate (PPi) and orthophosphate (Pi). The catalytic entity of MAT is a dimer. MAT cofactors are Mg+2 (or Co+2) and K+ ions<ref>PMID:8611562</ref>.

[[Image:Sam rxn 2.jpg|800px]]

The nucleophilic sulfur atom of methionine attacks the slightly positive 5' carbon of the adenosine sugar unit. Following this, the bond from the 5' carbon to the oxygen breaks, separating the tripolyphosphate from the newly formed S-adenosylmethionine (SAM) <ref name="Murray et al.">Murray B, Antonyuk SV, Marina A, Lu SC, Mato JM, Hasnain SS, Rojas Al. Crystallography captures catalytic steps in human methionine adenosyltransferase enzymes. PNAS. 2016 Feb 8;113 (8) 2104-2109. doi: https://doi.org/10.1073/pnas.1510959113</ref>. This is an example of an SN2 reaction, where the substrates move through a transition state to then form the products. The products are only released after the methionine binds and the C-O bond breaks.

== Structure ==
<StructureSection load='5a1i' size='400' side='right' caption='MAT dimer in complex with methionine, PPNP, and adenosine (PBD 5a1i)' scene=''>
MAT consists of α and β subunits. The MATα1 and <scene name='90/907472/Mat2a/4'>MATα2</scene> subunits are catalytic subunits while MATβ is a regulatory subunit. MATα2 subunits can form <scene name='49/493038/Tetramer/1'>tetramers</scene>, where the active site is found <scene name='49/493038/Tetramer/2'>between two of the subunits</scene>. The subunits are encoded on different genes in humans, so they are created separately and can then come together to form various complexes, such as MATαβ or MATα2 dimers <ref name="Murray et al." />. Not much is currently known about the function of this regulatory subunit and how it regulates the function of the enzyme<ref>DOI:10.1107/S2052252514012585</ref>. However, Murray et al.<ref name="Murray et al." /> show that even in the absence of the regulatory subunit, the active site found in the catalytic subunit remains functional.

The biological assembly of rat S-adenosylmethionine synthetase is a <scene name='49/493038/Cv/7'>homotetramer</scene>. The <scene name='49/493038/Cv/9'>active site of MAT is located between adjacent subunits</scene><ref>PMID:12888348</ref>. The <scene name='49/493038/Substrates/2'>substrates</scene> used by the enzyme are methionine and ATP. Notably, ATP is not used as a source of energy in this reaction like it is for many other processes. Instead, it is used as a substrate in the synthesis reaction. Methionine and ATP enter the active site and are stabilized by residues present there, including lysine and histidine. Once the reaction begins to take place, methionine flips toward the 5' carbon of the adenosine sugar<ref>doi:10.1042/BJ20121580</ref>. Following nucleophilic attack of the sulfur on the carbon, the C-O bond between the phosphates and the carbon breaks, and the <scene name='49/493038/Product/3'>products</scene> are formed (tripolyphosphate not pictured). SAM is released from the active site first. MAT also catalyzes hydrolysis of the tripolyphosphate into pyrophosphate and orthophosphate, which are then released from the active site <ref>Niland CN, Ghosh A, Cahill SM, Schramm VL. Mechanism and Inhibition of Human Methionine Adenosyltransferase 2A. ACS Biochemistry. 2021 Mar 3;60 (10) 791-801. doi: https://doi.org/10.1021/acs.biochem.0c00998</ref>.

== Gating Loop ==
MAT has been shown to have a <scene name='49/493038/Loop/6'>gating loop</scene> next to the active site <ref name="Murray et al." />.

<jmol>
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This structure is thought to allow access to the active site, becoming ordered or disordered. When the loop is ordered, the active site is closed, and it is opened again when the loop is disordered. Murray et al. <ref name="Murray et al." /> found that when SAM or adenosine is bound to the active site the gate is closed, and when PPNP (tripolyphosphate in the body) is bound to the active site the gate is open. It is still unknown what causes the gating loop to open and what triggers the release of products, but it is not caused by hydrolysis of tripolyphosphate <ref name="Murray et al." />. This finding shows that hydrolysis of tripolyphosphate does not provide energy for the opening of the gating loop, nor does ATP provide energy for any part of this reaction.
</StructureSection>

==3D structures of S-adenosylmethionine synthetase==

[[S-adenosylmethionine synthetase 3D structures]]

{{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|

*S-adenosylmethionine synthetase

**[[1fug]] – EcMAT – ''Escherichia coli''<br />
**[[3iml]] – MAT – ''Burkholderia pseudomallei''<br />
**[[2ydy]] – hMAT II subunit β – human<br />
**[[4le5]] – MAT- ''Campylobacter jejuni''<br />
**[[4hpv]] - SsMAT – ''Sulfolobus solfataricus''<br />
**[[3tde]] – MAT- ''Mycobacterium tuberculosis''<br />
**[[3s82]] – MAT- ''Mycobacterium avium''<br />
**[[3rv2]] – MAT- ''Mycobacterium marinum''<br />

*S-adenosylmethionine synthetase complexes

**[[1xra]], [[1xrb]] – EcMAT + Pi + K + Mg <br />
**[[1xrc]] - EcMAT + Pi + Co + K<br />
**[[1mxa]] - EcMAT + Pi + PPi + Mg + K<br />
**[[1mxb]] - EcMAT + Pi + ADP + Mg + K<br />
**[[1mxc]] - EcMAT + Pi + Br-ADP + Mg + K<br />
**[[1p7l]] – EcMAT + methionine + AdoMet + AMPPNP + Mg + K<br />
**[[1rg9]] - EcMAT + AdoMet + AMPPNP + Mg + K<br />
**[[1qm4]] - rMAT+ methionine analog + K + Mg – rat<br />
**[[1o90]] - rMAT + Pi + Mg + K<br />
**[[1o92]] – rMAT + methionine analog + ADP + Mg + K<br />
**[[1o93]] – rMAT + methionine analog + ATP + Mg + K<br />
**[[1o9t]] – rMAT + methionine + ADP + Mg + K<br />
**[[2obv]] – hMAT I + AdoMet + Na <br />
**[[2p02]] - hMAT II + AdoMet<br />
**[[2ydx]] – MAT + resveratrol + NADP + Ca + ADP derivative<br />
**[[4l2z]], [[4k0b]] - SsMAT + Pi + PPi + Mg + SAM derivative <br />
}}
== References ==
<references/>
[[Category:Topic Page]][[Category:One-carbon metabolism]]

Methionine adenosyltransferase

2022-04-25T14:54:59Z

Kia Yang:

[[Methionine adenosyltransferase]] (MAT) or S-adenosylmethionine synthetase (SAM synthetase) synthesizes S-adenosylmethionine (SAM or AdoMet) from the substrates adenosine triphosphate (ATP) and methionine. ATP isn’t used only as a source of energy like it is in other reactions but gets a methionine added onto the 5' carbon while the three phosphate groups are broken down and released from the active site. This enzyme is conserved and found in many organisms, so it is essential for life. Importantly, the production of SAM by MAT provides methyl for methylation of nucleic acids, allowing for epigenetic modification. Problems with this enzyme have been shown to cause diseases including various cancers.

== Relevance ==
The product of this enzymatic reaction, SAM, is the universal methyl donor of metabolism. DNA methyltransferases can transfer a methyl group from SAM to the 5th carbon of cytosine residues <ref>DOI:10.1038/npp.2012.112</ref>. In this way, MAT is indirectly important for regulation of gene expression by providing methyl through SAM. SAM is also involved in N-methylation, O-methylation and C-methylation, yielding S-adenosyl homocysteine as a product that gets recycled by the [[one-carbon metabolism]]. Radical SAM enzymes break down SAM into an adenosyl radical and methionine, enabling a host of otherwise difficult to achieve reactions, e.g. in molybdenum cofactors biosynthesis<ref>DOI:10.1073/pnas.0404624101</ref>. Accumulation of S-adenosyl homocysteine (or homocysteine itself) indicates an imbalance in supply and demand for SAM in the organism. Methionine metabolism impairment in liver diseases is related in alteration in MAT<ref>PMID:7741002</ref>.

== Function and reaction mechanism ==
'''S-adenosylmethionine synthetase''' or '''S-adenosylmethionine synthase''' or '''S-adenosylmethionine transferase''' or '''methionine adenosyltransferase''' (MAT) catalyzes the conversion of methionine and ATP to S-adenosylmethionine (AdoMet), pyrophosphate (PPi) and orthophosphate (Pi). The catalytic entity of MAT is a dimer. MAT cofactors are Mg+2 (or Co+2) and K+ ions<ref>PMID:8611562</ref>.

[[Image:Sam rxn 2.jpg|800px]]

The nucleophilic sulfur atom of methionine attacks the slightly positive 5' carbon of the adenosine sugar unit. Following this, the bond from the 5' carbon to the oxygen breaks, separating the tripolyphosphate from the newly formed S-adenosylmethionine (SAM) <ref name="Murray et al.">Murray B, Antonyuk SV, Marina A, Lu SC, Mato JM, Hasnain SS, Rojas Al. Crystallography captures catalytic steps in human methionine adenosyltransferase enzymes. PNAS. 2016 Feb 8;113 (8) 2104-2109. doi: https://doi.org/10.1073/pnas.1510959113</ref>. This is an example of an SN2 reaction, where the substrates move through a transition state to then form the products. The products are only released after the methionine binds and the C-O bond breaks.

== Structure ==
<StructureSection load='5a1i' size='400' side='right' caption='MAT dimer in complex with methionine, PPNP, and adenosine (PBD 5a1i)' scene=''>
MAT consists of α and β subunits. The MATα1 and <scene name='90/907472/Mat2a/4'>MATα2</scene> subunits are catalytic subunits while MATβ is a regulatory subunit. The subunits are encoded on different genes in humans, so they are created separately and can then come together to form various complexes, such as MATαβ or MATα2 dimers <ref name="Murray et al." />. Not much is currently known about the function of this regulatory subunit and how it regulates the function of the enzyme<ref>DOI:10.1107/S2052252514012585</ref>. However, Murray et al.<ref name="Murray et al." /> show that even in the absence of the regulatory subunit, the active site found in the catalytic subunit remains functional.

The biological assembly of rat S-adenosylmethionine synthetase is a <scene name='49/493038/Cv/7'>homotetramer</scene>. The <scene name='49/493038/Cv/8'>active site of MAT is located between adjacent subunits</scene><ref>PMID:12888348</ref>. The <scene name='90/907472/Substrates/2'>substrates</scene> used by the enzyme are methionine and ATP. Notably, ATP is not used as a source of energy in this reaction like it is for many other processes. Instead, it is used as a substrate in the synthesis reaction. Methionine and ATP enter the active site and are stabilized by residues present there, including lysine and histidine. Once the reaction begins to take place, methionine flips toward the 5' carbon of the adenosine sugar<ref>doi:10.1042/BJ20121580</ref>. Following nucleophilic attack of the sulfur on the carbon, the C-O bond between the phosphates and the carbon breaks, and the <scene name='90/907472/Product/3'>products</scene> are formed (tripolyphosphate not pictured). SAM is released from the active site first. MAT also catalyzes hydrolysis of the tripolyphosphate into pyrophosphate and orthophosphate, which are then released from the active site <ref>Niland CN, Ghosh A, Cahill SM, Schramm VL. Mechanism and Inhibition of Human Methionine Adenosyltransferase 2A. ACS Biochemistry. 2021 Mar 3;60 (10) 791-801. doi: https://doi.org/10.1021/acs.biochem.0c00998</ref>.

== Gating Loop ==
MAT has been shown to have a <scene name='49/493038/Loop/2'>gating loop</scene> next to the active site <ref name="Murray et al." />.

<jmol>
<jmolRadioGroup>
<item>
<script>model 1</script>
<text>ordered with SAM</text>
<checked>true</checked>
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<script>model 2</script>
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This structure is thought to allow access to the active site, becoming ordered or disordered. When the loop is ordered, the active site is closed, and it is opened again when the loop is disordered. Murray et al. <ref name="Murray et al." /> found that when SAM or adenosine is bound to the active site the gate is closed, and when PPNP (tripolyphosphate in the body) is bound to the active site the gate is open. It is still unknown what causes the gating loop to open and what triggers the release of products, but it is not caused by hydrolysis of tripolyphosphate <ref name="Murray et al." />. This finding shows that hydrolysis of tripolyphosphate does not provide energy for the opening of the gating loop, nor does ATP provide energy for any part of this reaction.
</StructureSection>

==3D structures of S-adenosylmethionine synthetase==
Scene 1: <scene name='49/493038/Tetramer/1'>tetramer</scene>
Scene 2:<scene name='49/493038/Tetramer/2'>binding site detail</scene>

[[S-adenosylmethionine synthetase 3D structures]]

{{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|

*S-adenosylmethionine synthetase

**[[1fug]] – EcMAT – ''Escherichia coli''<br />
**[[3iml]] – MAT – ''Burkholderia pseudomallei''<br />
**[[2ydy]] – hMAT II subunit β – human<br />
**[[4le5]] – MAT- ''Campylobacter jejuni''<br />
**[[4hpv]] - SsMAT – ''Sulfolobus solfataricus''<br />
**[[3tde]] – MAT- ''Mycobacterium tuberculosis''<br />
**[[3s82]] – MAT- ''Mycobacterium avium''<br />
**[[3rv2]] – MAT- ''Mycobacterium marinum''<br />

*S-adenosylmethionine synthetase complexes

**[[1xra]], [[1xrb]] – EcMAT + Pi + K + Mg <br />
**[[1xrc]] - EcMAT + Pi + Co + K<br />
**[[1mxa]] - EcMAT + Pi + PPi + Mg + K<br />
**[[1mxb]] - EcMAT + Pi + ADP + Mg + K<br />
**[[1mxc]] - EcMAT + Pi + Br-ADP + Mg + K<br />
**[[1p7l]] – EcMAT + methionine + AdoMet + AMPPNP + Mg + K<br />
**[[1rg9]] - EcMAT + AdoMet + AMPPNP + Mg + K<br />
**[[1qm4]] - rMAT+ methionine analog + K + Mg – rat<br />
**[[1o90]] - rMAT + Pi + Mg + K<br />
**[[1o92]] – rMAT + methionine analog + ADP + Mg + K<br />
**[[1o93]] – rMAT + methionine analog + ATP + Mg + K<br />
**[[1o9t]] – rMAT + methionine + ADP + Mg + K<br />
**[[2obv]] – hMAT I + AdoMet + Na <br />
**[[2p02]] - hMAT II + AdoMet<br />
**[[2ydx]] – MAT + resveratrol + NADP + Ca + ADP derivative<br />
**[[4l2z]], [[4k0b]] - SsMAT + Pi + PPi + Mg + SAM derivative <br />
}}
== References ==
<references/>
[[Category:Topic Page]][[Category:One-carbon metabolism]]

Methionine synthase

2022-04-25T12:42:30Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpeg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: Overall_methionine.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determine.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
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<checked>false</checked>
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<item>
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<text>both</text>
<checked>true</checked>
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As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene>, this is a 3D visual of the the binding domain of Cobalamin, with Cobalt(+1) in pink. Note here, Cobalamin contains a Corrin ring very similar to what we see in heme.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>, we can see where the DMB ligand exists. During its confirmation change, DMB will move away from the Corrin ring and replaced by His 757.

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
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<text>capped</text>
<checked>true</checked>
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<item>
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<text>with activation domain</text>
<checked>false</checked>
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</StructureSection>

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-25T12:41:00Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpeg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: Overall_methionine.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determine.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

In <scene name='90/907471/Bindingdomain1/1'>scene 1</scene> is the binding domain of Cobalamin, with Cobalt(+1) in pink.

In <scene name='90/907471/Bindingdomain2/1'>scene 2</scene>, we can see where the DMB ligand exists. During its confirmation change, DMB will move away from the Corrin ring and replaced by His 757.

In <scene name='90/907471/Bindingdomain3/2'>scene 3</scene>, Cobalt(+1) now accepts a methyl and forming Me-Cob(III)alamin.

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
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<text>with activation domain</text>
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</StructureSection>

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T15:26:57Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpeg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: Overall_methionine.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highly reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determine.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T15:25:55Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpeg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle.

== Oxidation States of Cobalamin ==

[[Image: Overall_methionine.gif]]

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determine.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T15:25:00Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpeg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated to Cob(I)alamin forming methylcobalamin (or Me-Cob(III)alamin). This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires the "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle.

[[Image: Overall_methionine.gif]]

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determine.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T15:22:40Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle to the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpeg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated. 5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

[[Image: Overall_methionine.gif]]

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determine.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T15:21:17Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle and the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpeg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine. MS uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction where the methyl group on N-5 from 5-me THF is donated. 5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

[[Image: Overall_methionine.gif]]

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determine.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T15:16:11Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle and the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpeg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine and uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction, as seen above, where the methyl group on N-5 from 5-me THF, is donated. 5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

[[Image: Overall_methionine.gif]]

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.
Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T15:14:31Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle and the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

[[Image:Overall.jpeg]]

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine and uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction, as seen above, where the methyl group on N-5 from 5-me THF, is donated. 5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

[[Image: Overall_methionine.gif]]

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.
Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<references/>
[[Category:One-carbon metabolism]]

<ref>DOI: 10.1128/JB.00208-06</ref>
<ref>DOI:10.1073/pnas.1133218100</ref>

Methionine synthase

2022-04-23T15:13:56Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

Addlt ref 1<ref>DOI: 10.1128/JB.00208-06</ref>

Addlt ref 2<ref>DOI:10.1073/pnas.1133218100</ref>

[[Image:Overall.jpeg]]

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle and the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

==Function==

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine and uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction, as seen above, where the methyl group on N-5 from 5-me THF, is donated. 5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

[[Image: Overall_methionine.gif]]

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.
Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T15:13:25Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

Addlt ref 1<ref>DOI: 10.1128/JB.00208-06</ref>

Addlt ref 2<ref>DOI:10.1073/pnas.1133218100</ref>

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle and the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

==Function==

[[Image:Overall.jpeg]]

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine and uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction, as seen above, where the methyl group on N-5 from 5-me THF, is donated. 5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

[[Image: Overall_methionine.gif]]

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-me THF donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.
Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T15:09:32Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

Addlt ref 1<ref>DOI: 10.1128/JB.00208-06</ref>

Addlt ref 2<ref>DOI:10.1073/pnas.1133218100</ref>

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle and the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

==Function==

[[Image:Overall.jpeg]]

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine and uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction, as seen above, where the methyl group on N-5 from 5-me THF, is donated. 5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

[[Image: Overall_methionine.gif]]

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-MTHFR donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.
Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===

<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<references/>
[[Category:One-carbon metabolism]]

File:Overall methionine.gif

2022-04-23T15:08:13Z

Kia Yang: Methionine synthase cycles

== Summary ==
Methionine synthase cycles
== Licensing ==
{{self|cc-by-sa-3.0,2.5,2.0,1.0|GFDL}}

Methionine synthase

2022-04-23T12:34:52Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

Addlt ref 1<ref>DOI: 10.1128/JB.00208-06</ref>

Addlt ref 2<ref>DOI:10.1073/pnas.1133218100</ref>

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle and the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

==Function==

[[Image:Overall.jpeg]]

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine and uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction, as seen above, where the methyl group on N-5 from 5-me THF, is donated. 5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-MTHFR donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized (as shown below in the darker yellow color) and now requires reduction and remethylation triggering the reactivation cycle. In the C-terminal, S-adenosylmethionine or SAM donates methyl with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.
Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===
<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T12:33:33Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

Addlt ref 1<ref>DOI: 10.1128/JB.00208-06</ref>

Addlt ref 2<ref>DOI:10.1073/pnas.1133218100</ref>

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle and the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

==Function==

[[Image:Overall.jpeg]]

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine and uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction, as seen above, where the methyl group on N-5 from 5-me THF, is donated. 5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-MTHFR donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. However, every 2,000 cycles or so, Cob(I)alamin becomes oxidized and requires reduction and remethylation. In the C-terminal, S-adenosylmethionine or SAM donates methyl in the reactivation cycle with Flavodoxin as the electron donor<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.
Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===
<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
</item>
<item>
<script>anim off; delay 1.0; model 0;</script>
<text>both</text>
<checked>false</checked>
</item>
<item>
<script>anim fps 1; anim mode loop; anim on;</script>
<text>animate</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

</StructureSection>

== References ==

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T12:29:47Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

Addlt ref 1<ref>DOI: 10.1128/JB.00208-06</ref>

Addlt ref 2<ref>DOI:10.1073/pnas.1133218100</ref>

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle and the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5- me THF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

==Function==

[[Image:Overall.jpeg]]

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine and uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction, as seen above, where the methyl group on N-5 from 5-me THF, is donated. 5-me THF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-MTHFR donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. In the C-terminal, S-adenosylmethionine or SAM donates methyl in the reactivation cycle<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.
Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
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<checked>false</checked>
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<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
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</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===
<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
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<text>capped</text>
<checked>true</checked>
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<text>with activation domain</text>
<checked>false</checked>
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</StructureSection>

== References ==

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-23T12:27:55Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

Addlt ref 1<ref>DOI: 10.1128/JB.00208-06</ref>

Addlt ref 2<ref>DOI:10.1073/pnas.1133218100</ref>

'''Methionine synthase''' (MS; EC: 2.1.1.13) is the enzyme in [[one-carbon metabolism]] linking the folate cycle and the methionine cycle. MS catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate (5-MTHF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies. As it is used as a methyl donor in the form of S-adenosylmethionine, the resulting homocysteine is recyled to form methionine again.

==Function==

[[Image:Overall.jpeg]]

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine and uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction, as seen above, where the methyl group on N-5 from 5-MTHF, is donated. 5-MTHF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref> as a methyl carrier.

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>
=== Domain organization ===

Methionine synthase contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier. In the N-terminal, 5-MTHFR donates a methyl in the catalytic cycle to Cob(I)alamin, which then donates it to homocysteine to form methionine. In the C-terminal, S-adenosylmethionine or SAM donates methyl in the reactivation cycle<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>.

[[Image:Methionine synthase domains.gif]]

The full structure of MS has yet to be determined.
Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

=== Cobalamin binding ===

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

<scene name='90/907471/Bindingdomain1/1'>scene 1</scene>

<scene name='90/907471/Bindingdomain2/1'>scene 2</scene>

<scene name='90/907471/Bindingdomain3/2'>scene 3</scene>

=== Cobalamin activation ===
<scene name='90/907471/B12_activation_w_sah/1'>B12 activation</scene>. This structure uses the mutant H759G to maximise the fraction of enzyme with the B12 domain in the cap-off conformation bound to the activation domain. The approach of the B12 domain and the activation domain has to be carefully regulated because methylating homocysteine with methyl groups from S-adenosyl methionine results in a futile cycle. Thus, this step should be reserved to rescue B12 out of the +2 cobalt oxidation state, and then methylation of homocysteine using a methyl group from 5-me THF resumes.

=== Cap domain ===

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the <scene name='90/907471/Cap/5'>imidazole side chain containing His 759</scene> replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand triad that increases the efficiency of the methyl transfer during the catalytic cycle (not shown). With His on, the cap is on Cobalamin. When interacting with the activation domain, there is no room for the cap, and the cobalamin moves a bit out of the reach of the histidine (in the crystal structure, they used the His759Gly mutation to favor the His-off conformation).<ref name="Bandarian et al"/>.

<jmol>
<jmolRadioGroup>
<item>
<script>anim off; delay 1.0; model 2</script>
<text>capped</text>
<checked>true</checked>
</item>
<item>
<script>anim off; delay 1.0; model 1</script>
<text>with activation domain</text>
<checked>false</checked>
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</StructureSection>

== References ==

<references/>
[[Category:One-carbon metabolism]]

Methionine synthase

2022-04-22T14:12:07Z

Kia Yang:

This page is being worked on during the Spring 2022 semester.

Addlt ref 1<ref>DOI: 10.1128/JB.00208-06</ref>

Addlt ref 2<ref>DOI:10.1073/pnas.1133218100</ref>

'''Methionine synthase''' (MS; EC: 2.1.1.13) is an important enzyme in [[one-carbon metabolism]]. MS catalyzes the transfer of a methyl group from methyltetrahydrofolate (MTHF) to homocysteine, resulting in the formation of methionine. Methionine is an essential amino acid required by our bodies for healthy cell and tissue growth. It is essential as it is not naturally derived in our bodies, thus requiring the conversion of homocysteine to methionine as needed.

==Function==

[[Image:Overall.jpeg]]

MS is a B12-dependent enzyme responsible for regenerating methionine from homocysteine and uses vitamin B12 Cobalamin as a cofactor. The change from homocysteine to methionine is an SN2 reaction, as seen above, where the methyl group on N-5 from methyltetrahydrofolate (MTHF), is donated. MTHF is a product of methylenetetrahydrofolate reductase [[MTHFR]] from the folate cycle. This is a complex reaction as tetrahydrofolate (THF), the product, is a poor leaving group and requires a "super nucleophile", vitamin B12 Cob(I)alamin, to carry out the reaction<ref>DOI:10.1146/annurev.biochem.72.121801.161828</ref><ref name="Kung et al">DOI: 10.1038/nature10916</ref>; the methyl carrier.

== Relevance ==

MS is an important enzyme responsible for generating methionine, required by our bodies for healthy cell and tissue growth, and protein synthesis. Any MS and/or B12 deficiencies can result in diseases such as abnormal birth defects or anemia<ref name="Kung et al"/>.

Uses in treating cancer.

== Structural highlights ==
<StructureSection load='1bmt' size='310' side='right' caption='Homodimer of B12 binding domain of MS. Cobalt in pink.' scene=''>

The full structure of MS has yet to be determined but studies have found it contains four domains, each with a unique function that bind to Cob(I)alamin as the methyl carrier, MTHF as the methyl donor in the catalytic cycle, homocysteine as the methyl acceptor, and S-adenosylmethionine or SAM, as the methyl donor in the reactivation cycle<ref name="Bandarian et al">DOI: 10.1038/nsb738</ref>. The orientation of the domains changes during the catalytic cycle.

Shown here is the <scene name='90/907471/Superposition/7'>theoretical prediction</scene> of the structure by the alphafold algorithm, with experimental structures of the N-terminal 2 domains as well as of the C-terminal 2 domins superposed.

<jmol>
<jmolRadioGroup>
<item>
<script>hide 1.1</script>
<text>experimental fragments</text>
<checked>false</checked>
</item>
<item>
<script>display 1.1</script>
<text>theoretical</text>
<checked>false</checked>
</item>
<item>
<script>display all</script>
<text>both</text>
<checked>true</checked>
</item>
</jmolRadioGroup>
</jmol>

As the graph below shows, the prediction has high confidence in the internal structure of individual domains but not the relative orientation.

[[Image:Position error alphafold P13009.jpg|400px]]

During each cycle, the domains must be positioned close enough to Cobalamin in order for methyl transfers to be successful. Conformations of MS allows substrates to be presented to Cobalamin for reactions to occur.

== Vitamin B12 ==

[[Image:cob_1_alamin.jpeg|500px]]

The vitamin B12 Cobalamin binding domain has a special characteristic in that, it is most naturally found in a protective conformation to prevent unwanted chemistry from occurring (PDB: 1BMT). This is referred to as a 'capping' mechanism.

== Cap domain ==

When B12 is not engaged with one of the other three substrate binding domains, it is protected by a <scene name='90/907471/Cap/1'>cap</scene>.

In the Cob(I)alamin binding domain, the imidazole side chain containing His 759 replaces the dimethylbenzimidazole (DMB) ligand. His 759 bonds to Asp 757 and Ser 810 via hydrogen bonds to create a ligand trifecta that increases the efficiency of the methyl transfer during the catalytic cycle. With His on, the cap is off of Cobalamin to allow for it to hold onto the methyl from MTHF. With His off, the cap is on thus no reaction.<ref name="Bandarian et al"/>.

== Oxidation States of Cobalamin ==

Cobalamin exists in three different oxidation states during the MS cycle.

'''Cob(I)alamin''': Cobalt in the +1 oxidation state is nicknamed the "super nucleophile" as its high energy is required to carry out the complex SN2 reaction of breaking the bond between THF and the methyl group, in the catalytic cycle.

'''Co(III)alamin''': Cobalt in +3 oxidation state occurs when His 759 replaces the dimethylbenzimidazole (DMB) ligand to allow for the methyl to be accepted by Cob(I)alamin, forming Me-Cob(III)alamin.

'''Cob(II)alamin''': Cob(I)alamin is highlight reactive towards oxygen so occasionally under aerobic conditions, Cob(I)alamin will occasionally undergo oxidation leading to an inactive Cob(II)alamin enzyme in the +2 oxidation state. This is regulated by reductive methylation by using Flavodoxin as an electron donor to reactivate Cob(I)alamin, and subsequently regenerates Me-Cob(III)alamin with a methyl being donated from SAM.

</StructureSection>

== References ==

<references/>
[[Category:One-carbon metabolism]]