Crystal structure of the external aldimine of Citrobacter freundii methionine γ-lyase with glycine provides insight in mechanisms of two stages of physiological reaction and isotope exchange of α- and β-protons of competitive inhibitors

The three-dimensional structure of the external aldimine of Citrobacter freundii methionine gamma-lyase with competitive inhibitor glycine has been determined at 2.45 A resolution. It revealed subtle conformational changes providing effective binding of the inhibitor and facilitating labilization of C alpha-protons of the external aldimine. The structure shows that 1, 3-prototropic shift of C alpha-proton to C4'-atom of the cofactor may proceed with participation of active site Lys210 residue whose location is favorable for performing this transformation by a concerted mechanism. The observed stereoselectivity of isotopic exchange of enantiotopic C alpha-protons of glycine may be explained on the basis of external aldimine structure. The exchange of C alpha-pro-(R)-proton of the external aldimine might proceed in the course of the concerted transfer of the proton from C alpha-atom of glycine to C4'-atom of the cofactor. The exchange of C alpha-pro-(S)proton may be performed with participation of Tyr113 residue which should be present in its basic form. The isotopic exchange of beta-protons, which is observed for amino acids bearing longer side groups, may be effected by two catalytic groups: Lys210 in its basic form, and Tyr113 acting as a general acid. (C) 2014 Elsevier Masson SAS. All rights reserved.