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

Structure. 2000 Sep 15;8(9):971-80. doi: 10.1016/s0969-2126(00)00188-x.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Aminopeptidases / chemistry*
  • Bacillus / enzymology
  • Bacterial Proteins*
  • Binding Sites
  • Carboxypeptidases / chemistry
  • Carrier Proteins / chemistry
  • Crystallography, X-Ray
  • Dimerization
  • Hexosyltransferases*
  • Models, Molecular
  • Molecular Sequence Data
  • Muramoylpentapeptide Carboxypeptidase / chemistry
  • Ochrobactrum anthropi / enzymology*
  • Penicillin-Binding Proteins
  • Peptidyl Transferases*
  • Protein Structure, Secondary
  • Streptomyces / enzymology
  • beta-Lactamases / chemistry


  • Bacterial Proteins
  • Carrier Proteins
  • Penicillin-Binding Proteins
  • Peptidyl Transferases
  • Hexosyltransferases
  • Carboxypeptidases
  • Aminopeptidases
  • Muramoylpentapeptide Carboxypeptidase
  • beta-Lactamases

Associated data

  • PDB/1EI5