5JJV

Crystal structure of XerH site-specific recombinase bound to palindromic difH substrate: post-cleavage complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending.

Bebel, A., Karaca, E., Kumar, B., Stark, W.M., Barabas, O.

(2016) Elife 5

  • DOI: 10.7554/eLife.19706
  • Primary Citation of Related Structures:  
    5JK0, 5JJV

  • PubMed Abstract: 

    • Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicoba ...

    Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicobacter pylori XerH with its recombination site DNA dif H , representing pre-cleavage and post-cleavage synaptic intermediates in the recombination pathway. The structures reveal that activation of DNA strand cleavage and rejoining involves large conformational changes and DNA bending, suggesting how interaction with the cell division protein FtsK may license recombination at the septum. Together with biochemical and in vivo analysis, our structures also reveal how a small sequence asymmetry in dif H defines protein conformation in the synaptic complex and orchestrates the order of DNA strand exchanges. Our results provide insights into the catalytic mechanism of Xer recombination and a model for regulation of recombination activity during cell division.

    Organizational Affiliation: 

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine recombinase XerH A, B363Helicobacter pylori 26695Mutation(s): 0 
Gene Names: xerH, HP_0675
Find proteins for O25386 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25386 
Go to UniProtKB:  O25386
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3')C, E13Helicobacter pylori 26695
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3')D, F17Helicobacter pylori 26695
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.40 Å
      • R-Value Free: 0.220 
      • R-Value Work: 0.195 
      • R-Value Observed: 0.196 
      • Space Group: I 2 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 86.38α = 90
      b = 115.22β = 90
      c = 235.2γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XDSdata reduction
      XDSdata scaling
      autoSHARPphasing
      PHENIXmodel building

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History 

      Deposition Data

      • Deposited Date: 2016-04-25 
      • Released Date: 2016-12-28 
        • Deposition Author(s): Bebel, A., Barabas, O.

      Revision History 

      • Version 1.0: 2016-12-28
        Type: Initial release
      • Version 1.1: 2017-01-11
        Changes: Database references
      • Version 1.2: 2018-09-19
        Changes: Advisory, Data collection, Database references