Crystal structure of DNA polymerase sliding clamp from Bacillus subtilis

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Differential Modes of Peptide Binding onto Replicative Sliding Clamps from Various Bacterial Origins.

Wolff, P.Amal, I.Olieric, V.Chaloin, O.Gygli, G.Ennifar, E.Lorber, B.Guichard, G.Wagner, J.Dejaegere, A.Burnouf, D.Y.

(2014) J Med Chem 57: 7565-7576

  • DOI: https://doi.org/10.1021/jm500467a
  • Primary Citation of Related Structures:  
    4TR6, 4TR7, 4TR8, 4TSZ

  • PubMed Abstract: 

    Bacterial sliding clamps are molecular hubs that interact with many proteins involved in DNA metabolism through their binding, via a conserved peptidic sequence, into a universally conserved pocket. This interacting pocket is acknowledged as a potential molecular target for the development of new antibiotics. We previously designed short peptides with an improved affinity for the Escherichia coli binding pocket. Here we show that these peptides differentially interact with other bacterial clamps, despite the fact that all pockets are structurally similar. Thermodynamic and modeling analyses of the interactions differentiate between two categories of clamps: group I clamps interact efficiently with our designed peptides and assemble the Escherichia coli and related orthologs clamps, whereas group II clamps poorly interact with the same peptides and include Bacillus subtilis and other Gram-positive clamps. These studies also suggest that the peptide binding process could occur via different mechanisms, which depend on the type of clamp.

  • Organizational Affiliation

    Université de Strasbourg , UPR9002, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15, rue René Descartes, 67084 Strasbourg, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase III subunit beta
A, B
380Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: dnaNdnaGBSU00020
Find proteins for P05649 (Bacillus subtilis (strain 168))
Explore P05649 
Go to UniProtKB:  P05649
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05649
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.22α = 65.77
b = 68.33β = 82.84
c = 85.31γ = 86.79
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations