3ETL

RadA recombinase from Methanococcus maripaludis in complex with AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conservation of a conformational switch in RadA recombinase from Methanococcus maripaludis.

Li, Y.He, Y.Luo, Y.

(2009) Acta Crystallogr.,Sect.D 65: 602-610

  • DOI: 10.1107/S0907444909011871
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Archaeal RadAs are close homologues of eukaryal Rad51s ( approximately 40% sequence identity). These recombinases promote ATP hydrolysis and a hallmark strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. Pa ...

    Archaeal RadAs are close homologues of eukaryal Rad51s ( approximately 40% sequence identity). These recombinases promote ATP hydrolysis and a hallmark strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. Pairing of the 3'-overhangs located at the damaged DNA with a homologous double-stranded DNA enables the re-synthesis of the damaged region using the homologous DNA as the template. In recent studies, conformational changes in the DNA-interacting regions of Methanococcus voltae RadA have been correlated with the presence of activity-stimulating potassium or calcium ions in the ATPase centre. The series of crystal structures of M. maripaludis RadA presented here further suggest the conservation of an allosteric switch in the ATPase centre which controls the conformational status of DNA-interacting loops. Structural comparison with the distant Escherichia coli RecA homologue supports the notion that the conserved Lys248 and Lys250 residues in RecA play a role similar to that of cations in RadA. The conservation of a cationic bridge between the DNA-interacting L2 region and the terminal phosphate of ATP, together with the apparent stability of the nucleoprotein filament, suggests a gap-displacement model which may explain the advantage of ATP hydrolysis for DNA-strand exchange.


    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 maripaludisMutation(s): 1 
Gene Names: radA
Find proteins for P0CW58 (Methanococcus maripaludis)
Go to UniProtKB:  P0CW58
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 81.100α = 90.00
b = 81.100β = 90.00
c = 108.500γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-10-08 
  • Released Date: 2009-05-05 
  • Deposition Author(s): Li, Y., He, Y., Luo, Y.

Revision History 

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance