The structural basis for peptide selection by the transport receptor OppA

EMBO J. 2009 May 6;28(9):1332-40. doi: 10.1038/emboj.2009.65. Epub 2009 Mar 19.

Abstract

Oligopeptide-binding protein A (OppA) from Lactococcus lactis binds peptides of an exceptionally wide range of lengths (4-35 residues), with no apparent sequence preference. Here, we present the crystal structures of OppA in the open- and closed-liganded conformations. The structures directly explain the protein's phenomenal promiscuity. A huge cavity allows binding of very long peptides, and a lack of constraints for the position of the N and C termini of the ligand is compatible with binding of peptides with varying lengths. Unexpectedly, the peptide's amino-acid composition (but not the exact sequence) appears to have a function in selection, with a preference for proline-rich peptides containing at least one isoleucine. These properties can be related to the physiology of the organism: L. lactis is auxotrophic for branched chain amino acids and favours proline-rich caseins as a source of amino acids. We propose a new mechanism for peptide selection based on amino-acid composition rather than sequence.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism*
  • Carrier Proteins / chemistry*
  • Carrier Proteins / metabolism*
  • Crystallography, X-Ray
  • Lactococcus lactis / chemistry*
  • Lactococcus lactis / metabolism*
  • Lipoproteins / chemistry*
  • Lipoproteins / metabolism*
  • Mass Spectrometry
  • Models, Molecular*
  • Peptides / chemistry*
  • Peptides / metabolism*
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Structure-Activity Relationship

Substances

  • Bacterial Proteins
  • Carrier Proteins
  • Lipoproteins
  • Peptides
  • oligopeptide-binding protein, bacteria

Associated data

  • PDB/3DRF
  • PDB/3DRG
  • PDB/3DRH
  • PDB/3DRI
  • PDB/3DRJ
  • PDB/3DRK