3DTE

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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This is version 1.1 of the entry. See complete history. 


Literature

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: 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IrrE proteinA301Deinococcus desertiMutation(s): 0 
Gene Names: irrE
EC: 3.4.24
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.053α = 90
b = 52.813β = 90
c = 64.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing

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