Rational design of Meso-2,3-butanediol dehydrogenase by molecular dynamics simulation and experimental evaluations.

Zhongji Pu, Fangling Ji, Jingyun Wang, Yue Zhang, Wenhui Sun, Yongming Bao

Journal: FEBS letters 2017;591(20):3402-3413

PMID: 28875495

Abstract

Meso-2,3-butanediol dehydrogenase (meso-2,3-BDH) catalyzes NAD -dependent conversion of meso-2,3-butanediol to acetoin, a crucial external energy storage molecule in fermentive bacteria. In this study, the active tunnel of meso-2,3-BDH was identified. The two short α helixes positioned away from the α4-helix possibly expose the hydrophobic ligand-binding cavity, gating the exit of product and cofactor from the activity pocket. Further MM/GBSA-binding free energy analysis shows that Phe212 and Asn146 function as the key product-release sites. Site-directed mutagenesis experiments targeted to the sites show that the k of Phe212Tyr is enhanced up to (4-8)-fold. The original activity of Asn146Gln is retained, but the activity of Asn146Ala mutation is lost. These results could provide helpful guidance on rational design of short-chain dehydrogenases/reductases.

Address: School of Life Science and Biotechnology, Dalian University of Technology, China.; School of Food and Environment Science and Engineering, Dalian University of Technology, Panjin, China.

DOI: 10.1002/1873-3468.12834