The Crystal Structure of HucR from Deinococcus radiodurans

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.239 

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The Crystal Structure of the Transcriptional Regulator HucR from Deinococcus radiodurans Reveals a Repressor Preconfigured for DNA Binding.

Bordelon, T.Wilkinson, S.P.Grove, A.Newcomer, M.E.

(2006) J Mol Biol 360: 168-177

  • DOI: https://doi.org/10.1016/j.jmb.2006.05.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We report here the 2.3 A resolution structure of the hypothetical uricase regulator (HucR) from Deinococcus radiodurans R1. HucR, a member of the MarR family of DNA-binding proteins, was previously shown to repress its own expression as well as that of a uricase, a repression that is alleviated both in vivo and in vitro upon binding uric acid, the substrate for uricase. As uric acid is a potent scavenger of reactive oxygen species, and as D. radiodurans is known for its remarkable resistance to DNA-damaging agents, these observations indicate a novel oxidative stress response mechanism. The crystal structure of HucR in the absence of ligand or DNA reveals a dimer in which the DNA recognition helices are preconfigured for DNA binding. This configuration of DNA-binding domains is achieved through an apparently stable dimer interface that, in contrast to what is observed in other MarR homologs for which structures have been determined, shows little conformational heterogeneity in the absence of ligand. An additional amino-terminal segment, absent from other MarR homologs, appears to brace the principal helix of the dimerization interface. However, although HucR is preconfigured for DNA binding, the presence of a stacked pair of symmetry-related histidine residues at a central pivot point in the dimer interface suggests a mechanism for a conformational change to attenuate DNA binding.

  • Organizational Affiliation

    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
transcriptional regulator, MarR family
A, B
181Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RV71 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RV71 
Go to UniProtKB:  Q9RV71
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RV71
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.239 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.991α = 90
b = 44.991β = 90
c = 284.5γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations