3DRF

Lactococcal OppA complexed with an endogenous peptide in the closed conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1038/emboj.2009.65
  • Primary Citation of Related Structures:  

  • 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-liga ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligopeptide-binding protein oppA
A
590Lactococcus lactis subsp. cremoris (strain MG1363)Mutation(s): 0 
Gene Names: oppA
Find proteins for A2RJ53 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RJ53
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
endogenous peptide
B
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.131 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.114α = 90.00
b = 74.650β = 90.00
c = 115.445γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SHARPphasing
XSCALEdata scaling
REFMACrefinement
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-05
    Type: Database references