Crystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family.

TitleCrystal structure of a D-aminopeptidase from Ochrobactrum anthropi, a new member of the 'penicillin-recognizing enzyme' family.
Publication TypeJournal Article
Year of Publication2000
AuthorsBompard-Gilles, C., H. Remaut, V. Villeret, T. Prangé, L. Fanuel, M. Delmarcelle, B. Joris, J. Frère, and J. Van Beeumen
Date Published2000 Sep 15
KeywordsAmino Acid Sequence, Aminopeptidases, Bacillus, Bacterial Proteins, beta-Lactamases, Binding Sites, Carboxypeptidases, Carrier Proteins, Crystallography, X-Ray, Dimerization, Hexosyltransferases, Models, Molecular, Molecular Sequence Data, Muramoylpentapeptide Carboxypeptidase, Ochrobactrum anthropi, Penicillin-Binding Proteins, Peptidyl Transferases, Protein Structure, Secondary, Streptomyces

BACKGROUND: beta-Lactam compounds are the most widely used antibiotics. They inactivate bacterial DD-transpeptidases, also called penicillin-binding proteins (PBPs), involved in cell-wall biosynthesis. The most common bacterial resistance mechanism against beta-lactam compounds is the synthesis of beta-lactamases that hydrolyse beta-lactam rings. These enzymes are believed to have evolved from cell-wall DD-peptidases. Understanding the biochemical and mechanistic features of the beta-lactam targets is crucial because of the increasing number of resistant bacteria. DAP is a D-aminopeptidase produced by Ochrobactrum anthropi. It is inhibited by various beta-lactam compounds and shares approximately 25% sequence identity with the R61 DD-carboxypeptidase and the class C beta-lactamases.RESULTS: The crystal structure of DAP has been determined to 1.9 A resolution using the multiple isomorphous replacement (MIR) method. The enzyme folds into three domains, A, B and C. Domain A, which contains conserved catalytic residues, has the classical fold of serine beta-lactamases, whereas domains B and C are both antiparallel eight-stranded beta barrels. A loop of domain C protrudes into the substrate-binding site of the enzyme.CONCLUSIONS: Comparison of the biochemical properties and the structure of DAP with PBPs and serine beta-lactamases shows that although the catalytic site of the enzyme is very similar to that of beta-lactamases, its substrate and inhibitor specificity rests on residues of domain C. DAP is a new member of the family of penicillin-recognizing proteins (PRPs) and, at the present time, its enzymatic specificity is clearly unique.

Alternate JournalStructure
PubMed ID10986464