1OK7

A Conserved protein binding-site on Bacterial Sliding Clamps


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Biochemical Analysis of Sliding Clamp/Ligand Interactions Suggest a Competition between Replicative and Translesion DNA Polymerases

Burnouf, D.Y.Olieric, V.Wagner, J.Fujii, S.Reinbolt, J.Fuchs, R.P.P.Dumas, P.

(2004) J.Mol.Biol. 335: 1187


  • PubMed Abstract: 
  • Most DNA polymerases interact with their cognate processive replication factor through a small peptide, this interaction being absolutely required for their function in vivo. We have solved the crystal structure of a complex between the beta sliding ...

    Most DNA polymerases interact with their cognate processive replication factor through a small peptide, this interaction being absolutely required for their function in vivo. We have solved the crystal structure of a complex between the beta sliding clamp of Escherichia coli and the 16 residue C-terminal peptide of Pol IV (P16). The seven C-terminal residues bind to a pocket located at the surface of one beta monomer. This region was previously identified as the binding site of another beta clamp binding protein, the delta subunit of the gamma complex. We show that peptide P16 competitively prevents beta-clamp-mediated stimulation of both Pol IV and alpha subunit DNA polymerase activities, suggesting that the site of interaction of the alpha subunit with beta is identical with, or overlaps that of Pol IV. This common binding site for delta, Pol IV and alpha subunit is shown to be formed by residues that are highly conserved among many bacterial beta homologs, thus defining an evolutionarily conserved hydrophobic crevice for sliding clamp ligands and a new target for antibiotic drug design.


    Related Citations: 
    • Three-Dimensional Structure of the Beta Subunit of Escherichia Coli DNA Polymerase III Holoenzyme: A Sliding DNA Clamp
      Kong, X.-P.,Onrust, R.,O'Donnell, M.,Kuriyan, J.
      (1992) Cell 69: 425


    Organizational Affiliation

    UPR 9003 CNRS, IRCAD, 1 place de l'Hôpital, BP 424, 67091 Strasbourg, France. dominique.burnouf@ircad.u-strasbg.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE III
A, B
366Escherichia coli (strain K12)Gene Names: dnaN
EC: 2.7.7.7
Find proteins for P0A988 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A988
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE IV
C
16Escherichia coli (strain K12)Gene Names: dinB (dinP)
EC: 2.7.7.7
Find proteins for Q47155 (Escherichia coli (strain K12))
Go to UniProtKB:  Q47155
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.230α = 73.11
b = 65.220β = 85.58
c = 73.380γ = 85.80
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-15
    Type: Initial release
  • Version 1.1: 2013-02-13
    Type: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2015-09-16
    Type: Database references, Source and taxonomy, Structure summary