4TR7

Crystal structure of DNA polymerase sliding clamp from Mycobaterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit betaA, B402Mycobacterium tuberculosis CDC1551Mutation(s): 0 
Gene Names: dnaNMT0002
EC: 2.7.7.7
UniProt
Find proteins for P9WNU0 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore P9WNU0 
Go to UniProtKB:  P9WNU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNU0
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.49α = 63.58
b = 83.65β = 86.84
c = 84.03γ = 85.2
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

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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