4LD0

T. thermophilus RuvC in complex with Holliday junction substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.75 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.270 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of RuvC resolvase in complex with Holliday junction substrate.

Gorecka, K.M.Komorowska, W.Nowotny, M.

(2013) Nucleic Acids Res 41: 9945-9955

  • DOI: 10.1093/nar/gkt769
  • Primary Citation of Related Structures:  
    4LD0

  • PubMed Abstract: 
  • The key intermediate in genetic recombination is the Holliday junction (HJ), a four-way DNA structure. At the end of recombination, HJs are cleaved by specific nucleases called resolvases. In Gram-negative bacteria, this cleavage is performed by RuvC ...

    The key intermediate in genetic recombination is the Holliday junction (HJ), a four-way DNA structure. At the end of recombination, HJs are cleaved by specific nucleases called resolvases. In Gram-negative bacteria, this cleavage is performed by RuvC, a dimeric endonuclease that belongs to the retroviral integrase superfamily. Here, we report the first crystal structure of RuvC in complex with a synthetic HJ solved at 3.75 Å resolution. The junction in the complex is in an unfolded 2-fold symmetrical conformation, in which the four arms point toward the vertices of a tetrahedron. The two scissile phosphates are located one nucleotide from the strand exchange point, and RuvC approaches them from the minor groove side. The key protein-DNA contacts observed in the structure were verified using a thiol-based site-specific cross-linking approach. Compared with known complex structures of the phage resolvases endonuclease I and endonuclease VII, the RuvC structure exhibits striking differences in the mode of substrate binding and location of the cleavage site.


    Organizational Affiliation

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109, Warsaw, Poland.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Crossover junction endodeoxyribonuclease RuvCAB169Thermus thermophilus HB8Mutation(s): 1 
Gene Names: ruvCTTHA1090
EC: 3.1.22.4
Find proteins for Q5SJC4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SJC4 
Go to UniProtKB:  Q5SJC4
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA 31-MERC31N/A
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA 13-MERD13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNA 11-MERF11N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.75 Å
      • R-Value Free: 0.329 
      • R-Value Work: 0.267 
      • R-Value Observed: 0.270 
      • Space Group: P 32 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 106.356α = 90
      b = 106.356β = 90
      c = 132.653γ = 120
      Software Package:
      Software NamePurpose
      MAR345data collection
      PHASERphasing
      PHENIXrefinement
      XDSdata reduction
      XDSdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2013-09-04
        Type: Initial release
      • Version 1.1: 2013-09-18
        Changes: Database references
      • Version 1.2: 2013-12-04
        Changes: Database references
      • Version 1.3: 2017-11-15
        Changes: Refinement description