3Q4J

Structure of a small peptide ligand bound to E.coli DNA sliding clamp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-based design of short peptide ligands binding onto the E. coli processivity ring.

Wolff, P.Olieric, V.Briand, J.P.Chaloin, O.Dejaegere, A.Dumas, P.Ennifar, E.Guichard, G.Wagner, J.Burnouf, D.Y.

(2011) J.Med.Chem. 54: 4627-4637

  • DOI: 10.1021/jm200311m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The multimeric DNA sliding clamps confer high processivity to replicative DNA polymerases and are also binding platforms for various enzymes involved in DNA metabolism. These enzymes interact with the clamp through a small peptide that binds into a h ...

    The multimeric DNA sliding clamps confer high processivity to replicative DNA polymerases and are also binding platforms for various enzymes involved in DNA metabolism. These enzymes interact with the clamp through a small peptide that binds into a hydrophobic pocket which is a potential target for the development of new antibacterial compounds. Starting from a generic heptapeptide, we used a structure-based strategy to improve the design of new peptide ligands. Chemical modifications at specific residues result in a dramatic increase of the interaction as measured by SPR and ITC. The affinity of our best hits was improved by 2 orders of magnitude as compared to the natural ligand, reaching 10(-8) M range. The molecular basis of the interactions was analyzed by solving the co-crystal structures of the most relevant peptides bound to the clamp and reveals how chemical modifications establish new contacts and contributes to an increased affinity of the ligand.


    Organizational Affiliation

    Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit beta
A, B, C, D, E, F
366Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dnaN
Find proteins for P0A988 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A988
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide ligand
H, I, J, K, L
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
H, I, J, K, L
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 35.090α = 62.73
b = 132.870β = 88.51
c = 137.270γ = 89.77
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
DENZOdata reduction
BUSTERrefinement
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Other
  • Version 1.2: 2013-03-13
    Type: Other
  • Version 1.3: 2013-03-20
    Type: Database references