2FE3

The crystal structure of bacillus subtilis PerR-Zn reveals a novel Zn(Cys)4 Structural redox switch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the apo-PerR-Zn protein from Bacillus subtilis.

Traore, D.A.K.El Ghazouani, A.Ilango, S.Dupuy, J.Jacquamet, L.Ferrer, J.-L.Caux-Thang, C.Duarte, V.Latour, J.M.

(2006) Mol.Microbiol. 61: 1211-1219

  • DOI: 10.1111/j.1365-2958.2006.05313.x

  • PubMed Abstract: 
  • Bacteria adapt to elevated levels of Reactive Oxygen Species (ROS) by increasing the expression of defence and repair proteins, which is regulated by ROS responsive transcription factors. In Bacillus subtilis the zinc protein PerR, a peroxide sensor ...

    Bacteria adapt to elevated levels of Reactive Oxygen Species (ROS) by increasing the expression of defence and repair proteins, which is regulated by ROS responsive transcription factors. In Bacillus subtilis the zinc protein PerR, a peroxide sensor that binds DNA in the presence of a regulatory metal Mn2+ or Fe2+, mediates the adaptive response to H2O2. This study presents the first crystal structure of apo-PerR-Zn which shows that all four cysteine residues of the protein are involved in zinc co-ordination. The Zn(Cys)4 site locks the dimerization domain and stabilizes the dimer. Sequence alignment of PerR-like proteins supports that this structural site may constitute a distinctive feature of this class of peroxide stress regulators.


    Organizational Affiliation

    DRDC/Laboratoire de Physicochimie des Métaux en Biologie, UMR 5155 CEA-CNRS-UJF, CEA-Grenoble, 38054 Grenoble Cedex 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxide operon regulator
A, B
145Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: perR (ygaG)
Find proteins for P71086 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P71086
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.290α = 82.18
b = 42.160β = 80.11
c = 53.490γ = 60.96
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SOLVEphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-12-15 
  • Released Date: 2006-12-19 
  • Deposition Author(s): Traore, D.A.K.

Revision History 

  • Version 1.0: 2006-12-19
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance