Crystal structures of cobalamin-independent methionine synthase complexed with zinc, homocysteine, and methyltetrahydrofolate

Cobalamin-independent methionine synthase (MetE) catalyzes the synthesis of methionine by a direct transfer of the methyl group of N-5-methyltetrahydrofolate (CH3-H(4)PteGlu(n)) to the sulfur atom of homocysteine (Hcy). We report here the first crystal structure of this metalloenzyme under different forms, free or complexed with the Hcy and folate substrates. The Arabidopsis thaliana MetE (AtMetE) crystals reveal a monomeric structure built by two (betaalpha)(8) barrels making a deep groove at their interface. The active site is located at the surface of the C-terminal domain, facing the large inter-domain cleft. Inside the active site, His(647), Cys(649), and Cys(733) are involved in zinc coordination, whereas Asp(605), Ile(437), and Ser(439) interact with Hcy. Opposite the zinc/Hcy binding site, a cationic loop (residues 507-529) belonging to the C-terminal domain anchors the first glutamyl residue of CH3-H(4)PteGlu(5). The pterin moiety of CH3-H(4)PteGlu(5) is stacked with Trp(567), enabling the N-5-methyl group to protrude in the direction of the zinc atom. These data suggest a structural role of the N-terminal domain of AtMetE in the stabilization of loop 507-529 and in the interaction with the poly-glutamate chain of CH3-H(4)PteGlu(n). Comparison of AtMetE structures reveals that the addition of Hcy does not lead to a direct coordination of the sulfur atom with zinc but to a reorganization of the zinc binding site with a stronger coordination to Cys(649), Cys(733), and a water molecule.