2PFJ

Crystal Structure of T7 Endo I resolvase in complex with a Holliday Junction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.267 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structural basis of Holliday junction resolution by T7 endonuclease I.

Hadden, J.M.Declais, A.C.Carr, S.B.Lilley, D.M.Phillips, S.E.

(2007) Nature 449: 621-624

  • DOI: 10.1038/nature06158

  • PubMed Abstract: 
  • The four-way (Holliday) DNA junction is the central intermediate in homologous recombination, a ubiquitous process that is important in DNA repair and generation of genetic diversity. The penultimate stage of recombination requires resolution of the ...

    The four-way (Holliday) DNA junction is the central intermediate in homologous recombination, a ubiquitous process that is important in DNA repair and generation of genetic diversity. The penultimate stage of recombination requires resolution of the DNA junction into nicked-duplex species by the action of a junction-resolving enzyme, examples of which have been identified in a wide variety of organisms. These enzymes are nucleases that are highly selective for the structure of branched DNA. The mechanism of this selectivity has, however, been unclear in the absence of structural data. Here we present the crystal structure of the junction-resolving enzyme phage T7 endonuclease I in complex with a synthetic four-way DNA junction. Although the enzyme is structure-selective, significant induced fit occurs in the interaction, with changes in the structure of both the protein and the junction. The dimeric enzyme presents two binding channels that contact the backbones of the junction's helical arms over seven nucleotides. These interactions effectively measure the relative orientations and positions of the arms of the junction, thereby ensuring that binding is selective for branched DNA that can achieve this geometry.


    Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Endodeoxyribonuclease 1
A, B
149Escherichia phage T7Mutation(s): 1 
EC: 3.1.21.2
Find proteins for P00641 (Escherichia phage T7)
Go to UniProtKB:  P00641
Entity ID: 1
MoleculeChainsLengthOrganism
27-MERZ29N/A
Entity ID: 2
MoleculeChainsLengthOrganism
27-MERY29N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, Y, Z
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.267 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.977α = 90.00
b = 92.977β = 90.00
c = 124.265γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MxCuBEdata collection
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance