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

Abstract

Abstract 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 (CH 3 ‐H 4 folate) as the Me donor. Despite the absence of sequence homology, these enzymes employ very similar catalytic strategies. In each case, the p K a for the SH group of Hcy is lowered by coordination to Zn 2+ , which increases the concentration of the reactive thiolate at neutral pH. In each case, activation of CH 3 ‐H 4 folate appears to involve protonation at N(5). CH 3 ‐H 4 folate remains unprotonated in binary E⋅CH 3 ‐H 4 folate complexes, and protonation occurs only in the ternary E⋅CH 3 ‐H 4 folate⋅Hcy complex in MetE, or in the ternary E⋅CH 3 ‐H 4 folate⋅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.