| Summary: | A bioinformatic and phylogenetic study has been performed on a family of
penicillin–binding proteins including D–aminopeptidases, D–amino acid
amidases, DD–carboxypeptidases, and β –lactamases. Significant homology
between D–aminopeptidase from Ochrobactrum anthropi and other members
of the family has been shown and a number of conserved residues identified as S62, K65, Y153,
N155, H287, and G289. Three of those (Ser62, Lys65, and Tyr153) form a catalytic triangle
– the proton relay system that activates the generalized nucleophile in the course of
catalysis. Molecular modeling has indicated the conserved residue Lys65 to have an unusually
low pKa value, which has been confirmed experimentally by a study of the pH–profile of
D–aminopeptidase catalytic activity. The resulting data have been used to elucidate the
role of Lys65 in the catalytic mechanism of D–aminopeptidase as a general base for proton
transfer from catalytic Ser62 to Tyr153, and vice versa, during the
formation and hydrolysis of the acyl – enzyme intermediate.
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