2I1Q

RadA Recombinase in complex with Calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Calcium Stiffens Archaeal Rad51 Recombinase from Methanococcus voltae for Homologous Recombination.

Qian, X.He, Y.Ma, X.Fodje, M.N.Grochulski, P.Luo, Y.

(2006) J Biol Chem 281: 39380-39387

  • DOI: https://doi.org/10.1074/jbc.M607785200
  • Primary Citation of Related Structures:  
    2I1Q

  • PubMed Abstract: 

    Archaeal RadA or Rad51 recombinases are close homologues of eukaryal Rad51 and DMC1. These and bacterial RecA orthologues play a key role in DNA repair by forming helical nucleoprotein filaments in which a hallmark strand exchange reaction between homologous DNA substrates occurs. Recent studies have discovered the stimulatory role by calcium on human and yeast recombinases. Here we report that the strand exchange activity but not the ATPase activity of an archaeal RadA/Rad51 recombinase from Methanococcus voltae (MvRadA) is also subject to calcium stimulation. Crystallized MvRadA filaments in the presence of CaCl(2) resemble that of the recently reported ATPase active form in the presence of an activating dose of KCl. At the ATPase center, one Ca(2+) ion takes the place of two K(+) ions in the K(+)-bound form. The terminal phosphate of the nonhydrolyzable ATP analogue is in a staggered conformation in the Ca(2+)-bound form. In comparison, an eclipsed conformation was seen in the K(+)-bound form. Despite the changes in the ATPase center, both forms harbor largely ordered L2 regions in essentially identical conformations. These data suggest a unified stimulation mechanism by potassium and calcium because of the existence of a conserved ATPase center promiscuous in binding cations.


  • Organizational Affiliation

    Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair and recombination protein radA322Methanococcus voltaeMutation(s): 1 
Gene Names: RADA
UniProt
Find proteins for O73948 (Methanococcus voltae)
Explore O73948 
Go to UniProtKB:  O73948
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO73948
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.2α = 90
b = 84.2β = 90
c = 104.7γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MAR345data collection
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-24
    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: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description