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 

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

  • 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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Crossover junction endodeoxyribonuclease RuvC
A, B
169Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 1 
Gene Names: ruvC
EC: 3.1.22.4
Find proteins for Q5SJC4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJC4
Entity ID: 2
MoleculeChainsLengthOrganism
DNA 31-MERC31N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA 13-MERD13N/A
Entity ID: 4
MoleculeChainsLengthOrganism
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 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.356α = 90.00
b = 106.356β = 90.00
c = 132.653γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XDSdata scaling
PHASERphasing
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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