5LKM

RadA bound to dTDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Bacterial RadA is a DnaB-type helicase interacting with RecA to promote bidirectional D-loop extension.

Marie, L.Rapisarda, C.Morales, V.Berge, M.Perry, T.Soulet, A.L.Gruget, C.Remaut, H.Fronzes, R.Polard, P.

(2017) Nat Commun 8: 15638-15638

  • DOI: 10.1038/ncomms15638
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Homologous recombination (HR) is a central process of genome biology driven by a conserved recombinase, which catalyses the pairing of single-stranded DNA (ssDNA) with double-stranded DNA to generate a D-loop intermediate. Bacterial RadA is a conserv ...

    Homologous recombination (HR) is a central process of genome biology driven by a conserved recombinase, which catalyses the pairing of single-stranded DNA (ssDNA) with double-stranded DNA to generate a D-loop intermediate. Bacterial RadA is a conserved HR effector acting with RecA recombinase to promote ssDNA integration. The mechanism of this RadA-mediated assistance to RecA is unknown. Here, we report functional and structural analyses of RadA from the human pathogen Streptococcus pneumoniae. RadA is found to facilitate RecA-driven ssDNA recombination over long genomic distances during natural transformation. RadA is revealed as a hexameric DnaB-type helicase, which interacts with RecA to promote orientated unwinding of branched DNA molecules mimicking D-loop boundaries. These findings support a model of DNA branch migration in HR, relying on RecA-mediated loading of RadA hexamers on each strand of the recipient dsDNA in the D-loop, from which they migrate divergently to facilitate incorporation of invading ssDNA.


    Organizational Affiliation

    Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse F-31062, France.,Department of Structural Biology and Chemistry, G5 Biologie structurale de la sécrétion bactérienne, UMR 3528, CNRS/Institut Pasteur, Institut Pasteur, 25-28 rue du Docteur Roux, Paris 75015, France.,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, Brussels 1050, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA repair protein RadA
A, B, C
452Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Mutation(s): 0 
Gene Names: radA
EC: 3.6.4.-
Find proteins for Q8DRP0 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q8DRP0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYD
Query on TYD

Download SDF File 
Download CCD File 
A, B, C
THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 99.400α = 90.00
b = 169.900β = 90.00
c = 187.420γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
BUSTERrefinement
SHELXDEphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ERCFrance--

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release