title: Enzyme-substrate binding landscapes in the process of nitrile biodegradation mediated by nitrile hydratase and amidase.
abstract: The continuing discharge of nitriles in various industrial processes has caused serious environmental consequences of nitrile pollution. Microorganisms possess several nitrile-degrading pathways by direct interactions of nitriles with nitrile-degrading enzymes. However, these interactions are largely unknown and difficult to experimentally determine but important for interpretation of nitrile metabolisms and design of nitrile-degrading enzymes with better nitrile-converting activity. Here, we undertook a molecular modeling study of enzyme-substrate binding modes in the bi-enzyme pathway for degradation of nitrile to acid. Docking results showed that the top substrates having favorable interactions with nitrile hydratase from Rhodococcus erythropolis AJ270 (ReNHase), nitrile hydratase from Pseudonocardia thermophila JCM 3095 (PtNHase), and amidase from Rhodococcus sp. N-771 (RhAmidase) were benzonitrile, 3-cyanopyridine, and L-methioninamide, respectively. We further analyzed the interactional profiles of these top poses with corresponding enzymes, showing that specific residues within the enzyme's binding pockets formed diverse contacts with substrates. This information on binding landscapes and interactional profiles is of great importance for the design of nitrile-degrading enzyme mutants with better oxidation activity toward nitriles or amides in the process of pollutant treatments.
authors.affiliation: College of Environmental Science and Engineering, Hunan University, Changsha 410082, People's Republic of China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.forename: Zhuotong
authors.initials: Z
authors.lastname: Zeng
authors.forename: Guangming
authors.initials: G
authors.lastname: Zeng
authors.forename: Xuanming
authors.initials: X
authors.lastname: Liu
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
authors.forename: Lifeng
authors.initials: L
authors.lastname: Liu
authors.forename: Zhifeng
authors.initials: Z
authors.lastname: Liu
authors.forename: Gengxin
authors.initials: G
authors.lastname: Xie
mesh_terms: D000192:Actinomycetales / Q000201:enzymology*; D000581:Amidohydrolases / Q000737:chemistry*; D001665:Binding Sites; D001673:Biodegradation, Environmental; D003198:Computer Simulation; D004789:Enzyme Activation; D006836:Hydro-Lyases / Q000737:chemistry*; D008956:Models, Chemical; D009570:Nitriles / Q000737:chemistry* / Q000302:isolation & purification; D011485:Protein Binding; D012240:Rhodococcus / Q000201:enzymology*; D013379:Substrate Specificity; D014874:Water Pollutants, Chemical / Q000737:chemistry* / Q000302:isolation & purification; D018508:Water Purification / Q000379:methods
chemical_list: D009570:Nitriles; D014874:Water Pollutants, Chemical; D000581:Amidohydrolases; C019665:amidase; D006836:Hydro-Lyases; C048831:nitrile hydratase