The substrate specificity and the catalytic mechanism of N-carbamyl-d-amino acid amidohydrolase: A theoretical investigation

N-carbamyl-d-amino acid amidohydrolasecatalyzes the hydrolysis of N-carbamyl-d-amino acids to d-amino acids, ammonia and the carbon dioxide. The docking studies validate that d-NCAase possesses of preference for d-enantiomers, predict that Gly194 and Arg174 may take part in the catalytic mechanism, and Glu136 is essential to maintain the stable conformation for catalysis. The initial step of the acylation reaction catalyzed by d-NCAase has been studied by density functional calculations. It was furthermore demonstrated that Lys126, His143, and Asn196 decrease the reaction barrier, while Asn172 raise the barrier. The structural and mechanistic insights obtained from computational study should be valuable for the mechanisms of cysteine proteases.