title: Mechanistic study of manganese-substituted glycerol dehydrogenase using a kinetic and thermodynamic analysis.
abstract: Mechanistic insights regarding the activity enhancement of dehydrogenase by metal ion substitution were investigated by a simple method using a kinetic and thermodynamic analysis. By profiling the binding energy of both the substrate and product, the metal ion's role in catalysis enhancement was revealed. Glycerol dehydrogenase (GDH) from Klebsiella pneumoniae sp., which demonstrated an improvement in activity by the substitution of a zinc ion with a manganese ion, was used as a model for the mechanistic study of metal ion substitution. A kinetic model based on an ordered Bi-Bi mechanism was proposed considering the noncompetitive product inhibition of dihydroxyacetone (DHA) and the competitive product inhibition of NADH. By obtaining preliminary kinetic parameters of substrate and product inhibition, the number of estimated parameters was reduced from 10 to 4 for a nonlinear regression-based kinetic parameter estimation. The simulated values of time-concentration curves fit the experimental values well, with an average relative error of 11.5% and 12.7% for Mn-GDH and GDH, respectively. A comparison of the binding energy of enzyme ternary complex for Mn-GDH and GDH derived from kinetic parameters indicated that metal ion substitution accelerated the release of dioxyacetone. The metal ion's role in catalysis enhancement was explicated.
authors.affiliation: Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China; The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China.
authors.forename: Baishan
authors.initials: B
authors.lastname: Fang
authors.affiliation: Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Niu
authors.affiliation: Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Ren
authors.affiliation: Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
authors.forename: Yingxia
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China; The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China.
authors.forename: Shizhen
authors.initials: S
authors.lastname: Wang
mesh_terms: D002384:Catalysis; D007700:Kinetics; D007711:Klebsiella pneumoniae / Q000201:enzymology*; D008345:Manganese / Q000737:chemistry* / Q000378:metabolism; D008670:Metals / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity; D013401:Sugar Alcohol Dehydrogenases / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D008670:Metals; D008345:Manganese; D013401:Sugar Alcohol Dehydrogenases; C020672:glycerol dehydrogenase