6FVO

Mutant DNA polymerase sliding clamp from Mycobacterium tuberculosis with bound P7 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.689 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Peptide Interactions on Bacterial Sliding Clamps.

Andre, C.Martiel, I.Wolff, P.Landolfo, M.Lorber, B.Silva da Veiga, C.Dejaegere, A.Dumas, P.Guichard, G.Olieric, V.Wagner, J.G.Burnouf, D.Y.

(2019) Acs Infect Dis. --: --

  • DOI: 10.1021/acsinfecdis.9b00089
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial sliding clamps control the access of DNA polymerases to the replication fork and are appealing targets for antibacterial drug development. It is therefore essential to decipher the polymerase-clamp binding mode across various bacterial spec ...

    Bacterial sliding clamps control the access of DNA polymerases to the replication fork and are appealing targets for antibacterial drug development. It is therefore essential to decipher the polymerase-clamp binding mode across various bacterial species. Here, two residues of the E. coli clamp binding pocket, Ec S 346 and Ec M 362 , and their cognate residues in M. tuberculosis and B. subtilis clamps, were mutated. The effects of these mutations on the interaction of a model peptide with these variant clamps were evaluated by thermodynamic, molecular dynamics, X-rays crystallography, and biochemical analyses. Ec M 362 and corresponding residues in Gram positive clamps occupy a strategic position where a mobile residue is essential for an efficient peptide interaction. Ec S 346 has a more subtle function that modulates the pocket folding dynamics, while the equivalent residue in B. subtilis is essential for polymerase activity and might therefore be a Gram positive-specific molecular marker. Finally, the peptide binds through an induced-fit process to Gram negative and positive pockets, but the complex stability varies according to a pocket-specific network of interactions.


    Organizational Affiliation

    Université de Strasbourg , CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS , 15 rue René Descartes , F-67000 Strasbourg , France.,Institut Européen de Chimie et Biologie , Université de Bordeaux-CNRS UMR 5248, CBMN , 2, rue Robert Escarpit , 33607 Pessac , France.,Swiss Light Source (SLS) , Paul-Scherrer-Institute (PSI) , 5232 Villigen , Switzerland.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) , Département de Biologie Structurale et Génomique , 1 rue Laurent Fries , BP10142, 67404 Illkirch , France.,Biologie et Signalisation Cellulaire, ESBS , UMR7242 CNRS/Université de Strasbourg , Bld S. Brant , 67412 Illkirch Cedex , France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta sliding clamp
A, B, C, D
402Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Gene Names: dnaN
Find proteins for P9WNU0 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  P9WNU0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
P7 peptide
H, I, J, K
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALC
Query on ALC
H, I, J, K
L-PEPTIDE LINKINGC9 H17 N O2ALA
ACE
Query on ACE
H, I, J, K
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.689 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.210 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 78.488α = 68.64
b = 81.064β = 88.94
c = 90.015γ = 62.56
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
PDB_EXTRACTdata extraction
AutoPROCdata scaling
STARANISOdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
IMMIFrance2014013

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release