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 Å3) 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.

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► The 3-D structure model of NHase from R. ruber CGMCC3090 was built.
► The NHase with larger binding site cavity may catalyze a large variety of nitriles.
► The NHase had a preference for mono-nitriles rather than dinitriles.
► The studies provide experimental supports for enunciating the NHase functions.