Bidirectional Regulation of Nitrilase Reaction Specificity by Tuning the Characteristic Distances between Key Residues and Substrate

Nitrilases are a class of enzymes that hydrolyze nitriles to carboxylic acids and ammonia. However, as research has progressed, the hydration activities that convert nitriles to amides are also found in nitrilases from different sources, which result in difficulties for high-purity production of carboxylic acids and meanwhile endow the enzyme with potential for valuable amides biosynthesis. In this study, the distance between the residues Cys and Glu in the catalytic triad (DC-E), as well as that between the cyano group of nitrile substrates and Glu (DCN-E) were determined to coaffect the reaction pathway. A strategy of switching the characteristic distance “DC-E–DCN-E” of nitrilase was proposed to regulate its reaction specificity. By computer-aided in silico analysis and mutagenesis of hotspot residues, a triple mutant K200R/R224W/N246V and a hexamutant A87M/I91P/I136Q/M164V/R224S/V226R were obtained with strict hydrolysis and hydration activity, respectively. With phenylacetonitrile as a substrate, the content of phenylacetic acid produced by the triple mutant was increased from 50.9% to 98.5%, while that of phenylacetamide was increased from 49.1% to 96.4% by the hexamutant. The established computational design strategy provided important guidance to engineer nitrilases with inverse reaction specificity and meanwhile broadened their application fields.