3K70

Crystal structure of the complete initiation complex of RecBCD

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

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 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.

    Related Citations: 
    • Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks.
      Singleton, M.R., Dillingham, M.S., Gaudier, M., Kowalczykowski, S.C., Wigley, D.B.
      (2004) Nature 432: 187
    Organizational Affiliation: 

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exodeoxyribonuclease V beta chainA [auth B],
D [auth E]		1,180Escherichia coli K-12Mutation(s): 0 
Gene Names: b2820, JW2788, recB, rorA, ior
EC: 3.1.11.5
UniProt
Find proteins for P08394 (Escherichia coli (strain K12))
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Go to UniProtKB:  P08394
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UniProt GroupP08394
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exodeoxyribonuclease V gamma chainB [auth C],
E [auth F]		1,122Escherichia coli K-12Mutation(s): 0 
Gene Names: b2822, JW2790, recC
EC: 3.1.11.5
UniProt
Find proteins for P07648 (Escherichia coli (strain K12))
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Go to UniProtKB:  P07648
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UniProt GroupP07648
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exodeoxyribonuclease V alpha chainC [auth D],
F [auth G]		608Escherichia coli K-12Mutation(s): 0 
Gene Names: b2819, JW2787, recD, hopE
EC: 3.1.11.5
UniProt
Find proteins for P04993 (Escherichia coli (strain K12))
Explore P04993 
Go to UniProtKB:  P04993
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UniProt GroupP04993
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (46-MER)G [auth X],
H [auth Y]		51N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
I [auth B],
J [auth E]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.8α = 90
b = 192.9β = 90
c = 334.8γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description