Crystal structure of Lactococcal OppA co-crystallized with an octamer peptide in an open conformation

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

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This is version 1.3 of the entry. See complete history


The structural basis for peptide selection by the transport receptor OppA

Berntsson, R.P.-A.Doeven, M.K.Fusetti, F.Duurkens, R.H.Sengupta, D.Marrink, S.-J.Thunnissen, A.-M.Poolman, B.Slotboom, D.-J.

(2009) EMBO J 28: 1332-1340

  • DOI: https://doi.org/10.1038/emboj.2009.65
  • Primary Citation of Related Structures:  
    3DRF, 3DRG, 3DRH, 3DRI, 3DRJ, 3DRK

  • PubMed 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.

  • Organizational Affiliation

    Biochemistry Department, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oligopeptide-binding protein oppA590Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
Gene Names: oppAllmg_0701
Find proteins for A2RJ53 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore A2RJ53 
Go to UniProtKB:  A2RJ53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2RJ53
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide AASASA6N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.669α = 90
b = 123.224β = 101.9
c = 59.604γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-02-05
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description