Cobalamin‐Dependent and Cobalamin‐Independent Methionine Synthases: Are There Two Solutions to the Same Chemical Problem?

Two enzymes in Escherichia coli, cobalamin‐independent methionine synthase (MetE) and cobalamin‐dependent methionine synthase (MetH), catalyze the conversion of homocysteine (Hcy) to methionine using N(5)‐methyltetrahydrofolate (CH₃‐H₄folate) as the Me donor. Despite the absence of sequence homology, these enzymes employ very similar catalytic strategies. In each case, the pK_a for the SH group of Hcy is lowered by coordination to Zn²⁺, which increases the concentration of the reactive thiolate at neutral pH. In each case, activation of CH₃‐H₄folate appears to involve protonation at N(5). CH₃‐H₄folate remains unprotonated in binary E?CH₃‐H₄folate complexes, and protonation occurs only in the ternary E?CH₃‐H₄folate?Hcy complex in MetE, or in the ternary E?CH₃‐H₄folate?cob(I)alamin complex in MetH. Surprisingly, the similarities are proposed to extend to the structures of these two unrelated enzymes. The structure of a homologue of the Hcy‐binding region of MetH, betaine? homocysteine methyltransferase, has been determined. A search of the three‐dimensional‐structure data base by means of the structure‐comparison program DALI indicates similarity of the BHMT structure with that of uroporphyrin decarboxylase (UroD), a homologue of the MT2‐A and MT2‐M proteins from Archaea, which catalyze Me transfers from methylcorrinoids to coenzyme M and share the Zn‐binding scaffold of MetE. Here, we present a model for the Zn binding site of MetE, obtained by grafting the Zn ligands of MT2‐A onto the structure of UroD.