Crystal structure of the IRRE protein, a central regulator of DNA damage repair in deinococcaceae

Experimental Data Snapshot

  • Resolution: 3.50 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.245 

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Crystal structure of the IrrE protein, a central regulator of DNA damage repair in deinococcaceae

Vujicic-Zagar, A.Dulermo, R.Le Gorrec, M.Vannier, F.Servant, P.Sommer, S.de Groot, A.Serre, L.

(2009) J Mol Biol 386: 704-716

  • DOI: https://doi.org/10.1016/j.jmb.2008.12.062
  • Primary Citation of Related Structures:  
    3DTE, 3DTI, 3DTK

  • PubMed Abstract: 

    Deinococcaceae are famous for their extreme radioresistance. Transcriptome analysis in Deinococcus radiodurans revealed a group of genes up-regulated in response to desiccation and ionizing radiation. IrrE, a novel protein initially found in D. radiodurans, was shown to be a positive regulator of some of these genes. Deinococcus deserti irrE is able to restore radioresistance in a D. radiodurans DeltairrE mutant. The D. deserti IrrE crystal structure reveals a unique combination of three domains: one zinc peptidase-like domain, one helix-turn-helix motif and one GAF-like domain. Mutant analysis indicates that the first and third domains are critical regions for radiotolerance. In particular, mutants affected in the putative zinc-binding site are as sensitive to gamma and UV irradiation as the DeltairrE bacteria, and radioresistance is strongly decreased with the H217L mutation present in the C-terminal domain. In addition, modeling of IrrE-DNA interaction suggests that the observed IrrE structure may not bind double-stranded DNA through its central helix-turn-helix motif and that IrrE is not a classic transcriptional factor that activates gene expression by its direct binding to DNA. We propose that the putative protease activity of IrrE could be a key element of transcription enhancement and that a more classic transcription factor, possibly an IrrE substrate, would link IrrE to transcription of genes specifically involved in radioresistance.

  • Organizational Affiliation

    Laboratoire des Protéines Membranaires, Institut de Biologie Structurale UMR5075 (CEA/CNRS/Université Joseph Fourier), 41 rue Jules Horowitz, 38027 Grenoble Cedex 01, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IRRE protein301Deinococcus desertiMutation(s): 0 
Gene Names: irrE
Find proteins for C1CZ84 (Deinococcus deserti (strain DSM 17065 / CIP 109153 / LMG 22923 / VCD115))
Explore C1CZ84 
Go to UniProtKB:  C1CZ84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1CZ84
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

  • Resolution: 3.50 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.19α = 90
b = 53.41β = 90
c = 63.42γ = 90
Software Package:
Software NamePurpose
DNAdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description