2I1Q

RadA Recombinase in complex with Calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1074/jbc.M607785200

  • 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 ho ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA repair and recombination protein radA
A
322Methanococcus voltaeMutation(s): 1 
Gene Names: radA
Find proteins for O73948 (Methanococcus voltae)
Go to UniProtKB:  O73948
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

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Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.191 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 84.200α = 90.00
b = 84.200β = 90.00
c = 104.700γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
AMoREphasing
CNSrefinement
CNSphasing
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description