Molecular insights into substrate specificity of Rhodococcus ruber CGMCC3090 by gene cloning and homology modeling

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.