Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65850.49 
• Atom Count: 4397 
• Residue Count: 598 
• Unique protein chains: 2

3DRF

Lactococcal OppA complexed with an endogenous peptide in the closed conformation

• DOI: 10.2210/pdb3DRF/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Lactococcus lactis subsp. cremoris (strain MG1363)
• Expression System: Lactococcus lactis


• Deposited: 2008-07-11 Released: 2009-03-31 
• Deposition Author(s): Berntsson, R.P.-A., Doeven, M.K., Duurkens, R.H., Sengupta, D., Marrink, S.-J., Thunnissen, A.-M., Poolman, B., Slotboom, D.-J.

---

Experimental Data Snapshot

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

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

• PubMed: 19300437 
• DOI: 10.1038/emboj.2009.65
• Primary Citation of Related Structures:  
  3DRK, 3DRJ, 3DRI, 3DRH, 3DRG


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Oligopeptide-binding protein oppA	A	590	Lactococcus 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
Molecule	Chains	Sequence Length	Organism	Details
endogenous peptide	B	8	N/A	Mutation(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 = 59.114	α = 90.00
b = 74.650	β = 90.00
c = 115.445	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-11 
• Released Date: 2009-03-31 
• Deposition Author(s): Berntsson, R.P.-A., Doeven, M.K., Duurkens, R.H., Sengupta, D., Marrink, S.-J., Thunnissen, A.-M., Poolman, B., Slotboom, D.-J.

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