标题：Theoretical study on the proton shuttle mechanism of saccharopine dehydrogenase
作者：Sheng, Xiang; Gao, Jun; Liu, Yongjun; Liu, Chengbu
作者机构：[Sheng, Xiang; Gao, Jun; Liu, Yongjun; Liu, Chengbu] Shandong Univ, Sch Chem & Chem Engn, Key Lab Theoret & Computat Chem, Jinan 250100, Shandong, Peo 更多
通讯作者地址：[Liu, YJ]Shandong Univ, Sch Chem & Chem Engn, Key Lab Theoret & Computat Chem, Jinan 250100, Shandong, Peoples R China.
来源：JOURNAL OF MOLECULAR GRAPHICS & MODELLING
关键词：Saccharopine dehydrogenase; L-Lysine biosynthesis; Density functional; theory (DFT) method; Proton shuttle; Reaction mechanism
摘要：Saccharopine dehydrogenase (SDH) is the last enzyme in the AAA pathway of L-lysine biosynthesis. On the basis of crystal structures of SDH, the whole catalytic cycle of SDH has been studied by using density functional theory (DFT) method. Calculation results indicate that hydride transfer is the rate-limiting step with an energy barrier of 25.02 kcal/mol, and the overall catalytic reaction is calculated to be endothermic by 9.63 kcal/mol. Residue Lys77 is proved to be functional only in the process of saccharopine deprotonation until the formation of product L-lysine, and residue His96 is confirmed to take part in multiple proton transfer processes and can be described as a proton transfer station. From the point of view of energy, the SDH catalytic reaction for the synthesis of L-lysine is unfavorable compared with its reverse reaction for the synthesis of saccharopine. These results are essentially consistent with the experimental observations from pH dependence of kinetic parameters and isotope effects. (C) 2013 Elsevier Inc. All rights reserved.