3NTU

RADA RECOMBINASE D302K MUTANT IN COMPLEX with AMP-PNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

RAD51 protein ATP cap regulates nucleoprotein filament stability.

Amunugama, R.He, Y.Willcox, S.Forties, R.A.Shim, K.S.Bundschuh, R.Luo, Y.Griffith, J.Fishel, R.

(2012) J.Biol.Chem. 287: 8724-8736

  • DOI: 10.1074/jbc.M111.239426

  • PubMed Abstract: 
  • RAD51 mediates homologous recombination by forming an active DNA nucleoprotein filament (NPF). A conserved aspartate that forms a salt bridge with the ATP γ-phosphate is found at the nucleotide-binding interface between RAD51 subunits of the NPF know ...

    RAD51 mediates homologous recombination by forming an active DNA nucleoprotein filament (NPF). A conserved aspartate that forms a salt bridge with the ATP γ-phosphate is found at the nucleotide-binding interface between RAD51 subunits of the NPF known as the ATP cap. The salt bridge accounts for the nonphysiological cation(s) required to fully activate the RAD51 NPF. In contrast, RecA homologs and most RAD51 paralogs contain a conserved lysine at the analogous structural position. We demonstrate that substitution of human RAD51(Asp-316) with lysine (HsRAD51(D316K)) decreases NPF turnover and facilitates considerably improved recombinase functions. Structural analysis shows that archaebacterial Methanococcus voltae RadA(D302K) (MvRAD51(D302K)) and HsRAD51(D316K) form extended active NPFs without salt. These studies suggest that the HsRAD51(Asp-316) salt bridge may function as a conformational sensor that enhances turnover at the expense of recombinase activity.


    Organizational Affiliation

    Biophysics Graduate Program, Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University, Columbus, Ohio 43210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA repair and recombination protein radA
A
319Methanococcus voltaeMutation(s): 2 
Gene Names: radA
Find proteins for O73948 (Methanococcus voltae)
Go to UniProtKB:  O73948
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 84.970α = 90.00
b = 84.970β = 90.00
c = 104.320γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-07-05 
  • Released Date: 2011-07-27 
  • Deposition Author(s): Luo, Y.

Revision History 

  • Version 1.0: 2011-07-27
    Type: Initial release
  • Version 1.1: 2012-02-01
    Type: Database references
  • Version 1.2: 2012-10-17
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description