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 
  • R-Value Observed: 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

  • DOI: 10.1016/j.jmb.2003.11.049
  • Primary Citation of Related Structures:  
    1OK7

  • 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 clamp of Escherichia coli and the 16 residue C-terminal peptide of Pol IV (P16) ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASE IIIA, B366Escherichia coliMutation(s): 0 
EC: 2.7.7.7
UniProt
Find proteins for P0A988 (Escherichia coli (strain K12))
Explore P0A988 
Go to UniProtKB:  P0A988
Entity Groups  
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UniProt GroupP0A988
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASE IVC16Escherichia coliMutation(s): 0 
EC: 2.7.7.7
UniProt
Find proteins for Q47155 (Escherichia coli (strain K12))
Explore Q47155 
Go to UniProtKB:  Q47155
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47155
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.23α = 73.11
b = 65.22β = 85.58
c = 73.38γ = 85.8
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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