title: Molecular insights into substrate specificity of Rhodococcus ruber CGMCC3090 by gene cloning and homology modeling.
abstract: The primary aim of this study was to decipher the catalytic functions of the NHase with wide substrate spectra from Rhodococcus ruber CGMCC3090 by computer modeling and substrate docking. 3D structure model of the enzyme was built by computer modeling to obtain the optimal structure. The larger binding site cavity (559 Å(3)) indicated that this NHase may catalyze a large variety of substrates of nitriles. Some key residues such as αGlu82, αGln83, βTyr71, β Tyr72, β Arg52 and β Arg55 surrounding the binding site were unique compared with those of 3QXE as a template, indicating that the enzyme may have unusual substrate specificity. The docking and the biotransformation experiments demonstrated that the special docking pose and shorter distance proved to be more effective for the enzyme to improve function.
authors.affiliation: Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science and Technology), Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
authors.forename: Shiwei
authors.initials: S
authors.lastname: Wang
authors.forename: Yujie
authors.initials: Y
authors.lastname: Dai
authors.forename: Jianxin
authors.initials: J
authors.lastname: Wang
authors.forename: Yanbing
authors.initials: Y
authors.lastname: Shen
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhai
authors.forename: Heng
authors.initials: H
authors.lastname: Zheng
authors.forename: Min
authors.initials: M
authors.lastname: Wang
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D001711:Biotransformation; D002384:Catalysis; D020134:Catalytic Domain; D003001:Cloning, Molecular; D003198:Computer Simulation; D005798:Genes, Bacterial; D006836:Hydro-Lyases / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009570:Nitriles / Q000378:metabolism*; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000378:metabolism; D012240:Rhodococcus / Q000201:enzymology* / Q000235:genetics; D016415:Sequence Alignment; D017385:Sequence Homology; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D009570:Nitriles; D011994:Recombinant Proteins; D006836:Hydro-Lyases; C048831:nitrile hydratase