1RKM

STRUCTURE OF OPPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine.

Sleigh, S.H.Tame, J.R.Dodson, E.J.Wilkinson, A.J.

(1997) Biochemistry 36: 9747-9758

  • DOI: 10.1021/bi970457u
  • Primary Citation of Related Structures:  
    2RKM, 1RKM

  • PubMed Abstract: 
  • The periplasmic oligopeptide binding protein, OppA, acts as the initial receptor for the uptake of peptides by the oligopeptide permease (Opp) in Gram-negative bacteria. Opp will handle peptides between two and five amino acid residues regardless of their sequence ...

    The periplasmic oligopeptide binding protein, OppA, acts as the initial receptor for the uptake of peptides by the oligopeptide permease (Opp) in Gram-negative bacteria. Opp will handle peptides between two and five amino acid residues regardless of their sequence. The crystal structures of a series of OppA-peptide complexes have revealed an enclosed but versatile peptide binding pocket and have illustrated how tri- and tetrapeptide ligands are accommodated. Here, the crystal structures of (i) OppA complexed with a dipeptide (lysyllysine) and (ii) unliganded OppA have been solved using X-ray data extending to 1.8 and 2.4 A spacing, respectively. In the dipeptide complex, the alpha-amino group of the ligand is anchored through an ion pair interaction with Asp419, as observed in complexes with longer peptides. However, its alpha-carboxylate group forms water-mediated interactions with the guanidinium groups of Arg404 and Arg413 rather than the direct salt bridges to Arg413 and His371 observed in the tripeptide and tetrapeptide complexes, respectively. Isothermal titration calorimetric measurements of the binding of lysine-containing peptides of different lengths to OppA show that the dipeptide, KK, is bound with approximately 60-fold lower affinity than related tri- and tetrapeptides (KKK and KKKA, respectively). These data are discussed with reference to the calculated enthalpic and entropic contributions to ligand binding and the structures of the OppA peptide complexes. In the unliganded molecule, domain III has rotated as a rigid body through 26 degrees away from domains I and II, exposing the ligand binding site. The water structure in the binding cleft shows similarities to that in the various OppA-peptide complexes.


    Related Citations: 
    • The Role of Water in Sequence-Independent Ligand Binding by an Oligopeptide Transporter Protein
      Tame, J.R., Sleigh, S.H., Wilkinson, A.J., Ladbury, J.E.
      (1996) Nat Struct Biol 3: 998
    • Structure Determination of Oppa at 2.3 Angstroms Resolution Using Multiple Wavelength Anomalous Methods
      Glover, I.D., Denny, R., Nguti, N.D., Mcsweeney, S., Thompson, A., Dodson, E., Wilkinson, A.J., Tame, J.R.H.
      (1995) Acta Crystallogr D Biol Crystallogr 51: 39
    • The Crystal Structures of the Oligopeptide-Binding Protein Oppa Complexed with Tripeptide and Tetrapeptide Ligands
      Tame, J.R., Dodson, E.J., Murshudov, G., Higgins, C.F., Wilkinson, A.J.
      (1995) Structure 3: 1395
    • The Structural Basis of Sequence-Independent Peptide Binding by Oppa Protein
      Tame, J.R., Murshudov, G.N., Dodson, E.J., Neil, T.K., Dodson, G.G., Higgins, C.F., Wilkinson, A.J.
      (1994) Science 264: 1578

    Organizational Affiliation

    Department of Chemistry, University of York, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
OLIGO-PEPTIDE BINDING PROTEINA517Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Find proteins for P06202 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P06202 
Go to UniProtKB:  P06202
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.191 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.84α = 90
b = 97.84β = 90
c = 137.21γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
ROTAVATAdata reduction
AGROVATAdata reduction
AMoREphasing
REFMACrefinement
CCP4data scaling
ROTAVATA)data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-07-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance