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

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Abstract

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.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (21573127, 21373125, 21773138).

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  1. School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, Shandong, China

    Beibei Lin, Ge Tian & Yongjun Liu

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  1. Beibei Lin
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Correspondence to Yongjun Liu.

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214_2017_2140_MOESM1_ESM.docx

Supplementary material 1. Solvation model for the MD simulation; RMSDs for the protein backbone atoms along the MD trajectory; distances of some important hydrogen bonds in the MD simulation; superimposition of active sites of QM/MM optimized geometries of enzyme–substrate complexes; calculated QM/MM energy profile; optimized geometries of active site of IM2. (DOCX 1911 kb)

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Lin, B., Tian, G. & Liu, Y. Mechanistic insights into the γ-elimination reaction of l-methionine catalyzed by methionine γ-lyase (MGL). Theor Chem Acc 136, 105 (2017). https://doi.org/10.1007/s00214-017-2140-9

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