Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli

Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3472-7. doi: 10.1073/pnas.95.7.3472.


The structure of the proline-specific aminopeptidase (EC from Escherichia coli has been solved and refined for crystals of the native enzyme at a 2.0-A resolution, for a dipeptide-inhibited complex at 2.3-A resolution, and for a low-pH inactive form at 2.7-A resolution. The protein crystallizes as a tetramer, more correctly a dimer of dimers, at both high and low pH, consistent with observations from analytical ultracentrifuge studies that show that the protein is a tetramer under physiological conditions. The monomer folds into two domains. The active site, in the larger C-terminal domain, contains a dinuclear manganese center in which a bridging water molecule or hydroxide ion appears poised to act as the nucleophile in the attack on the scissile peptide bond of Xaa-Pro. The metal-binding residues are located in a single subunit, but the residues surrounding the active site are contributed by three subunits. The fold of the protein resembles that of creatine amidinohydrolase (creatinase, not a metalloenzyme). The C-terminal catalytic domain is also similar to the single-domain enzyme methionine aminopeptidase that has a dinuclear cobalt center.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aminopeptidases / chemistry
  • Aminopeptidases / genetics
  • Aminopeptidases / metabolism*
  • Binding Sites
  • Escherichia coli / enzymology*
  • Hydrogen-Ion Concentration
  • Molecular Sequence Data
  • Protein Conformation*
  • Structure-Activity Relationship
  • Substrate Specificity


  • Aminopeptidases
  • X-Pro aminopeptidase

Associated data

  • PDB/1A16
  • PDB/1AZ9
  • PDB/1JAW