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

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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 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.

Data availability

The following data sets were generated

1. Bebel A
2. Barabas O
(2016) Crystal structure of XerH site-specific recombinase bound to difH substrate: pre-cleavage complex
Publicly available at the RCSB Protein Data Bank (accession no: 5JK0).

http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5JK0
1. Bebel A
2. Barabas O
(2016) Crystal structure of XerH site-specific recombinase bound to palindromic difH substrate: post-cleavage complex
Publicly available at the RCSB Protein Data Bank (accession no: 5JJV).

http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5JJV

Article and author information

Author details

Aleksandra Bebel

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

Competing interests
The authors declare that no competing interests exist.
Ezgi Karaca

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

Competing interests
The authors declare that no competing interests exist.
Banushree Kumar

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

Competing interests
The authors declare that no competing interests exist.
W Marshall Stark

Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Orsolya Barabas

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

For correspondence
barabas@embl.de

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-2873-5872

Funding

European Molecular Biology Laboratory (Intramural Funds)

Aleksandra Bebel
Ezgi Karaca
Banushree Kumar
Orsolya Barabas

Alexander von Humboldt-Stiftung (Postdoctoral Fellowship)

Ezgi Karaca

EMBL International PhD Programme (Graduate Student Fellowship)

Aleksandra Bebel

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.