3DRF

Lactococcal OppA complexed with an endogenous peptide in the closed conformation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 

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:  
    3DRI, 3DRJ, 3DRK, 3DRF, 3DRG, 3DRH

  • 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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oligopeptide-binding protein oppAA590Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: oppA, llmg_0701
Find proteins for A2RJ53 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore A2RJ53 
Go to UniProtKB:  A2RJ53
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
endogenous peptideB8N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.114α = 90
b = 74.65β = 90
c = 115.445γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHARPphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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