title: Theoretical study on the proton shuttle mechanism of saccharopine dehydrogenase.
abstract: 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 25.02kcal/mol, and the overall catalytic reaction is calculated to be endothermic by 9.63kcal/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.
authors.affiliation: Key Laboratory of Theoretical and Computational Chemistry in Universities of Shandong, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Sheng
authors.forename: Jun
authors.initials: J
authors.lastname: Gao
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Liu
authors.forename: Chengbu
authors.initials: C
authors.lastname: Liu
mesh_terms: D008958:Models, Molecular; D008962:Models, Theoretical; D008968:Molecular Conformation; D011522:Protons; D011725:Pyridines / Q000737:chemistry; D012443:Saccharopine Dehydrogenases / Q000737:chemistry*; D012545:Schiff Bases / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D011522:Protons; D011725:Pyridines; D012545:Schiff Bases; C004649:carbinoxamine; D012443:Saccharopine Dehydrogenases
keywords: AAA; AMP; DAP; Density functional theory (DFT) method; NAD; NADH; OxGly; Proton shuttle; Reaction mechanism; SDH; Saccharopine dehydrogenase; adenosine monophosphate; diaminopimelate; l-Lysine biosynthesis; nicotinamide adenine dinucleotide [the + charge is omitted for convenience]; oxalylglycibe; reduced nicotinamide adenine dinucleotide; saccharopine dehydrogenase; α-Kg; α-aminoadipate; α-ketoglutarate