Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 84.77 kDa 
• Atom Count: 6602 
• Modelled Residue Count: 760 
• Deposited Residue Count: 760 
• Unique protein chains: 1

4TR6

Crystal structure of DNA polymerase sliding clamp from Bacillus subtilis

• PDB DOI: 10.2210/pdb4TR6/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-06-14 Released: 2014-09-10 
• Deposition Author(s): Burnouf, D., Olieric, V., Ennifar, E., Wolff, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.204 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

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

• PubMed: 25170813 
• 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. 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit beta	A, B	380	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: dnaN, dnaG, BSU00020 EC: 2.7.7.7
UniProt
Find proteins for P05649 (Bacillus subtilis (strain 168)) Explore P05649  Go to UniProtKB:  P05649

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.204 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.22	α = 65.77
b = 68.33	β = 82.84
c = 85.31	γ = 86.79

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-06-14 
• Released Date: 2014-09-10 
Deposition Author(s): Burnouf, D., Olieric, V., Ennifar, E., Wolff, P.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Database references