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Methionine synthase: Difference between revisions

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This page is being worked on during the Spring 2022 semester.
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'''Methionine synthase''' (MS; EC: 2.1.1.13) or '''5-methyltetrahydrofolate S-homocysteine methyltransferase''' 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.
'''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]]
[[Image:Overall.jpg]]


==Function==
== 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.
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.
5-me THF is a product of [[methylenetetrahydrofolate reductase]] ([[MTHFR]]) from the folate cycle.
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'''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.
'''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.
'''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.
'''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 ==
== Relevance ==
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== Structural highlights ==
== Structural highlights ==
<StructureSection load='1k7y' size='310' side='right' caption='C-terminal fragment of MS (PDB ID: 1k7y)' scene=''>
 
==Methionine synthase 3D structures==
 
[[Methionine synthase 3D structures]]
 
<StructureSection load='' size='400' side='right' scene='90/907471/Superposition_1/3'>
 
=== Domain organization ===
=== Domain organization ===


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The full structure of MS has yet to be determined.
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.
Shown here is the <scene name='90/907471/Superposition/8'>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>
<jmol>
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=== Cobalamin binding ===
=== Cobalamin binding ===


[[Image:cob_1_alamin.jpeg|500px]]
[[Image:cob_1_alamin.jpeg|300px]]
 
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 ===
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.


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.
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 ===
=== Cap domain ===
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   </jmolRadioGroup>
   </jmolRadioGroup>
</jmol>
</jmol>
=== 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>
</StructureSection>
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== References ==
== References ==


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


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

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Kia Yang, Karsten Theis, Michael O'Shaughnessy, Anna Postnikova, Michal Harel
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