Structure of an N-terminal truncation of Deinococcus radiodurans RecD2

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.235 

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This is version 1.2 of the entry. See complete history


DNA binding to RecD: role of the 1B domain in SF1B helicase activity.

Saikrishnan, K.Griffiths, S.P.Cook, N.Court, R.Wigley, D.B.

(2008) EMBO J 27: 2222-2229

  • DOI: https://doi.org/10.1038/emboj.2008.144
  • Primary Citation of Related Structures:  
    3E1S, 3K70

  • PubMed Abstract: 

    The molecular mechanism of superfamily 1Balpha helicases remains unclear. We present here the crystal structure of the RecD2 helicase from Deinococcus radiodurans at 2.2-A resolution. The structure reveals the folds of the 1B and 2B domains of RecD that were poorly ordered in the structure of the Escherichia coli RecBCD enzyme complex reported previously. The 2B domain adopts an SH3 fold which, although common in eukaryotes, is extremely rare in bacterial systems. In addition, the D. radiodurans RecD2 structure has aided us in deciphering lower resolution (3.6 A) electron density maps for the E. coli RecBCD enzyme in complex with a long DNA substrate that interacts with the RecD subunit. Taken together, these structures indicated an important role for the 1B domain of RecD, a beta-hairpin that extends from the surface of the 1A domain and interacts with the DNA substrate. On the basis of these structural data, we designed a mutant RecD2 helicase that lacks this pin. The 'pin-less' mutant protein is a fully active ssDNA-dependent ATPase but totally lacks helicase activity.

  • Organizational Affiliation

    Cancer Research UK Clare Hall Laboratories, The London Research Institute, Herts, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exodeoxyribonuclease V, subunit RecD574Deinococcus radioduransMutation(s): 0 
Gene Names: recD
Find proteins for Q9RT63 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RT63 
Go to UniProtKB:  Q9RT63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RT63
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.63α = 90
b = 89.63β = 90
c = 131.71γ = 90
Software Package:
Software NamePurpose
DNAdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references