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Rational design of Meso ‐2,3‐butanediol dehydrogenase by molecular dynamics simulation and experimental evaluations
Author(s) -
Pu Zhongji,
Ji Fangling,
Wang Jingyun,
Zhang Yue,
Sun Wenhui,
Bao Yongming
Publication year - 2017
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1002/1873-3468.12834
Subject(s) - acetoin , cofactor , mutagenesis , chemistry , stereochemistry , dehydrogenase , nad+ kinase , rational design , 2,3 butanediol , molecular dynamics , gating , enzyme , biochemistry , biophysics , mutation , computational chemistry , biology , nanotechnology , materials science , fermentation , gene
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 cat 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.