Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides

Abstract

Nitrile hydratase (NHase) is an enzyme containing non-corrin Co3+ in the non-standard active site. NHases from Pseudonocardia thermophila JCM 3095 catalyse hydration of nitriles to corresponding amides. The efficiency of the enzyme is 100 times higher for aliphatic nitriles then aromatic ones. In order to understand better this selectivity dockings of a series of aliphatic and aromatic nitriles and related amides into a model protein based on an X-ray structure were performed. Substantial differences in binding modes were observed, showing better conformational freedom of aliphatic compounds. Distinct interactions with postranslationally modified cysteines present in the active site of the enzyme were observed. Modeling shows that water molecule activated by a metal ion may easily directly attack the docked acrylonitrile to transform this molecule into acryloamide. Thus docking studies provide support for one of the reaction mechanisms discussed in the literature.

Modeling catalytic mechanism of nitrile hydratase by semi-empirical quantum mechanical calculation

“…In this reaction mechanism, the metal-bound -OH is assigned as the nucleophilic attacker, somewhat matching the outer-sphere mechanism in literatures [3,5,12]. Residue a-CEA 113 plays an important role for activating the active center, which is in consistent with experimental results of Hashimoto et al that site-directed mutagenesis of this residue would inactivate the enzyme [11].…”

“…Most recently, Peplowski et al performed autodocking studies of nitriles and amides into a Co-type NHase [12]. Their analyses of relative positions of crystallographic waters and the best-docked acrylonitrile indicated that the outer-sphere mechanism is more probable [12].…”

“…Most recently, Peplowski et al performed autodocking studies of nitriles and amides into a Co-type NHase [12]. Their analyses of relative positions of crystallographic waters and the best-docked acrylonitrile indicated that the outer-sphere mechanism is more probable [12]. Theoretical investigation by Hopmann et al showed that based on the first-shell mechanism in which the nitrile substrate binds directly to the low-spin iron in the sixth coordination site, the generally suggested role of the Fe(III) center as Lewis acid, activating the substrate toward nucleophilic attack, is shown to be unlikely [13].…”

Memetic algorithms for ligand expulsion from protein cavities

“…The NCA Charmm27 parameters and topology files were taken from Peplowski et al 44 . The NHase-NCA complex was solvated in (73Å×81Å×74Å) TIP3P water box and electrically neutralized by adding 0.15 mol/L sodium chloride ions.…”

A comparative DFT study of substrates and products of industrial enzyme nitrile hydratase

“…Neither the transition states in these enzymatic reactions nor in uncatalyzed hydration reactions are known yet. As the first step in the determination of reaction paths ligands-protein docking studies were performed and interactions of substrates and products with NHases were analyzed [12].…”