Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 83.09 kDa 
• Atom Count: 6235 
• Residue Count: 739 
• Unique protein chains: 2

1OK7

A Conserved protein binding-site on Bacterial Sliding Clamps

• DOI: 10.2210/pdb1OK7/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-07-18 Released: 2004-07-15 
• Deposition Author(s): Burnouf, D.Y., Olieric, V., Wagner, J., Fujii, S., Reinbolt, J., Fuchs, R.P.P., Dumas, P.

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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 

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

• PubMed: 14729336 
• DOI: 10.1016/j.jmb.2003.11.049
• Structures With Same Primary Citation


• 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). 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.

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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

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Organizational Affiliation: 

UPR 9003 CNRS, IRCAD, 1 place de l'Hôpital, BP 424, 67091 Strasbourg, France. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA POLYMERASE III	A, B	366	Escherichia coli	Mutation(s): 0  EC: 2.7.7.7
Find proteins for P0A988 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A988

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
DNA POLYMERASE IV	C	16	Escherichia coli	Mutation(s): 0  EC: 2.7.7.7
Find proteins for Q47155 (Escherichia coli (strain K12)) Go to UniProtKB:  Q47155

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 = 41.23	α = 73.11
b = 65.22	β = 85.58
c = 73.38	γ = 85.8

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-07-18 
• Released Date: 2004-07-15 
Deposition Author(s): Burnouf, D.Y., Olieric, V., Wagner, J., Fujii, S., Reinbolt, J., Fuchs, R.P.P., Dumas, P.

Revision History 

• 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