2RKM

STRUCTURE OF OPPA COMPLEXED WITH LYS-LYS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.167 

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:  

  • 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 ...

    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 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
    • 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.Mol.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.,Sect.D 51: 39


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OLIGO-PEPTIDE BINDING PROTEIN
A
517Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: oppA
Find proteins for P06202 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P06202
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IUM
Query on IUM

Download SDF File 
Download CCD File 
A
URANYL (VI) ION
O2 U
IZLHQJIUOZHTLW-UHFFFAOYSA-N
 Ligand Interaction
LYS
Query on LYS

Download SDF File 
Download CCD File 
A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 110.470α = 90.00
b = 77.150β = 90.00
c = 71.590γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CCP4data scaling
REFMACrefinement
DENZOdata reduction
CCP4data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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