3DRF

Lactococcal OppA complexed with an endogenous peptide in the closed conformation

Summary for 3DRF

• Entry DOI: 10.2210/pdb3drf/pdb
• Related: 3DRG 3DRH 3DRI 3DRJ 3DRK
• Descriptor: Oligopeptide-binding protein oppA, endogenous peptide (3 entities in total)
• Functional Keywords: oligo-peptide binding, voluminous binding cavity, venus fly-trap, peptide binding protein
• Biological source: Lactococcus lactis; More
• Total number of polymer chains: 2
• Total formula weight: 65850.49

Authors

Berntsson, R.P.-A.,Doeven, M.K.,Duurkens, R.H.,Sengupta, D.,Marrink, S.-J.,Thunnissen, A.-M.,Poolman, B.,Slotboom, D.-J. (deposition date: 2008-07-11, release date: 2009-03-31, Last modification date: 2024-03-20)

Primary citation

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.
The structural basis for peptide selection by the transport receptor OppA
Embo J., 28:1332-1340, 2009

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.

PubMed: 19300437
DOI: 10.1038/emboj.2009.65

Experimental method

X-RAY DIFFRACTION (1.3 Å)