4TSZ

Crystal structure of DNA polymerase sliding clamp from Pseudomonas aeruginosa with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit beta368Pseudomonas aeruginosaMutation(s): 0 
EC: 2.7.7.7
Find proteins for Q9I7C4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I7C4 
Go to UniProtKB:  Q9I7C4
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ACE-GLN-ALC-ASP-LEU-ZCL peptide6synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALC
Query on ALC
B [auth Q] , BA [auth 4] , D [auth R] , DA [auth 5] , F [auth S] , FA [auth 6] , H [auth T] , J [auth U] , 
B [auth Q],  BA [auth 4],  D [auth R],  DA [auth 5],  F [auth S],  FA [auth 6],  H [auth T],  J [auth U],  L [auth V],  N [auth X],  P [auth Y],  R [auth Z],  T [auth 0],  V [auth 1],  X [auth 2],  Z [auth 3]
L-PEPTIDE LINKINGC9 H17 N O2ALA
ZCL
Query on ZCL
B [auth Q] , BA [auth 4] , D [auth R] , DA [auth 5] , F [auth S] , FA [auth 6] , H [auth T] , J [auth U] , 
B [auth Q],  BA [auth 4],  D [auth R],  DA [auth 5],  F [auth S],  FA [auth 6],  H [auth T],  J [auth U],  L [auth V],  N [auth X],  P [auth Y],  R [auth Z],  T [auth 0],  V [auth 1],  X [auth 2],  Z [auth 3]
L-PEPTIDE LINKINGC9 H9 Cl2 N O2PHE
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001111
Query on PRD_001111
B [auth 0], BA [auth 1], D [auth 2], DA [auth 3], F [auth 4], FA [auth 5], H [auth 6], J [auth Q], L [auth R], N [auth S], P [auth T], R [auth U], T [auth V], V [auth X], X [auth Y], Zpeptide ligandOligopeptide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.982α = 90.01
b = 85.947β = 89.94
c = 272.202γ = 116.56
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: 2014-09-17
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.2: 2014-11-19
    Changes: Database references
  • Version 1.3: 2016-12-21
    Changes: Non-polymer description