Methionine synthase

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^[5]. The orientation of the domains changes during the catalytic cycle.

Shown here is the 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.

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

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

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 .

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.^[5].

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.