Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism.

ABSTRACT: Carboxypeptidase A is a zinc-containing enzyme that cleaves the C-terminal residue in a polypeptide substrate. Despite much experimental work, there is still a significant controversy concerning its catalytic mechanism. In this study, the carboxypeptidase A-catalyzed hydrolysis of the hippuryl-L-Phe molecule (k(cat) = 17.7 +/- 0.7 s(-1)) is investigated using both density functional theory and a hybrid quantum mechanical/molecular mechanical approach. The enzymatic reaction was found to proceed via a promoted-water pathway with Glu270 serving as the general base and general acid. Free-energy calculations indicate that the first nucleophilic addition step is rate-limiting, with a barrier of 17.9 kcal/mol. Besides activating the zinc-bound water nucleophile, the zinc cofactor also serves as

SUBMITTER: Xu D 

PROVIDER: S-EPMC2741171 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature