On the role of tyrosine as catalytic base in nitrile hydratase

Nitrile Hydratases (NHases) catalyze the conversion of nitriles to their corresponding amides. Two NHase classes exist, the Fe-III-NHases and the Co-III-NHases. Both harbour an intriguing active site, with a low-spin metal ion coordinated to deprotonated back-bone amides and oxidized cysteine residues. So far it has not been possible to conclusively determine the reaction mechanism of NHase. Here we employ density functional theory to investigate the recent proposal that a fully conserved second-shell tyrosine residue is the catalytic base of nitrile hydratase (J. Biol. Chem. 2007, 282, 7397-7404). In the proposed mechanism, the tyrosine is suggested to be in the tyrosinate state and to mediate nitrile hydration through activation of a water molecule, which attacks the metal-bound substrate. We have explored this mechanism employing quantum chemical active site models on the basis of the Co-III-NHase from P. thermophila JCM 3095 and the Fe-III-NHase from R. erythropolis N-771. Potential energy curves and optimized transition states are presented. The computed barriers for the two models are a few kcal/mol above the experimental value, indicating that the conserved second-shell tyrosine could function as the catalytic base of NHase. To further evaluate the likelihood of this mechanism, we estimated the pK(a) value of the second-shell tyrosine in each model. We also provide estimates of the energy involved in the exchange of a metal-bound water molecule with a nitrile substrate. (C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)