Mechanistic insights into the γ-elimination reaction of l -methionine catalyzed by methionine γ-lyase (MGL)

The γ-elimination mechanism of l-methionine catalyzed by methionine γ-lyase was studied by employing the combined quantum mechanics and molecular (QM/MM) calculations. Based on the two crystal structures of methionine γ-lyase from Clostridium sporogenes and Citrobacter freundii, a computational model that contains the enzyme and the external aldimine intermediate was constructed. According to the results of our calculations, the whole catalytic reaction can be divided into two parts. Part I describes the formation of external aldimine intermediate from the internal aldimine intermediate, in which the key protonation step within the tetrahedral intermediate (IM2) should require the assistance of one water molecule, and the dissociation of Lys210 from the internal aldimine intermediate corresponds to an overall energy barrier of 13.5 kcal/mol. In Part II, the external aldimine intermediate converts to the aminocrotonate intermediate, which contains complex asynchronous and concerted proton transfer processes, including those of Cα-proton and Cβ-proton of the substrate as well as the C4′-proton of PLP, in which the pocket residues Tyr113 and Lys210 play key roles. The abstraction of Cβ-proton and the transfer of C4′-proton correspond to very similar barrier heights (16.5 and 16.2 kcal/mol) on the potential energy surface, implying that both steps are possibly rate-limiting. Besides, the calculated overall energy barrier is close to the free energy barrier estimated from the experiment (16.3 kcal/mol). These results may provide useful information for further understanding the catalysis of pyridoxal 5′-phosphate (PLP)-dependent lyase.