2OWY

The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding

Ha, J.Y.Kim, H.K.Kim, D.J.Kim, K.H.Oh, S.J.Lee, H.H.Yoon, H.J.Song, H.K.Suh, S.W.

(2007) Nucleic Acids Res 35: 2671-2681

  • DOI: 10.1093/nar/gkm144
  • Primary Citation of Related Structures:  
    2OWY

  • PubMed Abstract: 
  • RecA plays a central role in the nonmutagenic repair of stalled replication forks in bacteria. RdgC, a recombination-associated DNA-binding protein, is a potential negative regulator of RecA function. Here, we have determined the crystal structure of RdgC from Pseudomonas aeruginosa ...

    RecA plays a central role in the nonmutagenic repair of stalled replication forks in bacteria. RdgC, a recombination-associated DNA-binding protein, is a potential negative regulator of RecA function. Here, we have determined the crystal structure of RdgC from Pseudomonas aeruginosa. The J-shaped monomer has a unique fold and can be divided into three structural domains: tip domain, center domain and base domain. Two such monomers dimerize to form a ring-shaped molecule of approximate 2-fold symmetry. Of the two inter-subunit interfaces within the dimer, one interface ('interface A') between tip/center domains is more nonpolar than the other ('interface B') between base domains. The structure allows us to propose that the RdgC dimer binds dsDNA through the central hole of approximately 30 A diameter. The proposed model is supported by our DNA-binding assays coupled with mutagenesis, which indicate that the conserved positively charged residues on the protein surface around the central hole play important roles in DNA binding. The novel ring-shaped architecture of the RdgC dimer has significant implications for its role in homologous recombination.


    Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Recombination-associated protein rdgCA, B306Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: rdgCPA3263
UniProt
Find proteins for Q9HYX7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HYX7 
Go to UniProtKB:  Q9HYX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HYX7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.494α = 90
b = 116.041β = 90
c = 76.028γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2007-02-17 
  • Released Date: 2007-11-20 
  • Deposition Author(s): Suh, S.W.

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description