Crystal structure of RecJ from Thermus thermophilus HB8

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.230 

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This is version 1.2 of the entry. See complete history


Structure of RecJ exonuclease defines its specificity for single-stranded DNA

Wakamatsu, T.Kitamura, Y.Kotera, Y.Nakagawa, N.Kuramitsu, S.Masui, R.

(2010) J Biol Chem 285: 9762-9769

  • DOI: https://doi.org/10.1074/jbc.M109.096487
  • Primary Citation of Related Structures:  
    2ZXO, 2ZXP, 2ZXR

  • PubMed Abstract: 

    RecJ is a single-stranded DNA (ssDNA)-specific 5'-3' exonuclease that plays an important role in DNA repair and recombination. To elucidate how RecJ achieves its high specificity for ssDNA, we determined the entire structures of RecJ both in a ligand-free form and in a complex with Mn(2+) or Mg(2+) by x-ray crystallography. The entire RecJ consists of four domains that form a molecule with an O-like structure. One of two newly identified domains had structural similarities to an oligonucleotide/oligosaccharide-binding (OB) fold. The OB fold domain alone could bind to DNA, indicating that this domain is a novel member of the OB fold superfamily. The truncated RecJ containing only the core domain exhibited much lower affinity for the ssDNA substrate compared with intact RecJ. These results support the hypothesis that these structural features allow specific binding of RecJ to ssDNA. In addition, the structure of the RecJ-Mn(2+) complex suggests that the hydrolysis reaction catalyzed by RecJ proceeds through a two-metal ion mechanism.

  • Organizational Affiliation

    Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Single-stranded DNA specific exonuclease RecJ666Thermus thermophilus HB8Mutation(s): 0 
Gene Names: recjTTHA1167
EC: 3.1.11
Find proteins for Q5SJ47 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJ47 
Go to UniProtKB:  Q5SJ47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJ47
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.230 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.984α = 90
b = 82.984β = 90
c = 249.223γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description