The Structure of Xis Reveals the Basis for Filament Formation and Insight Into DNA Bending Within a Mycobacteriophage Intasome

J Mol Biol. 2014 Jan 23;426(2):412-22. doi: 10.1016/j.jmb.2013.10.002. Epub 2013 Oct 7.


The recombination directionality factor, Xis, is a DNA bending protein that determines the outcome of integrase-mediated site-specific recombination by redesign of higher-order protein-DNA architectures. Although the attachment site DNA of mycobacteriophage Pukovnik is likely to contain four sites for Xis binding, Xis crystals contain five subunits in the asymmetric unit, four of which align into a Xis filament and a fifth that is generated by an unusual domain swap. Extensive intersubunit contacts stabilize a bent filament-like arrangement with Xis monomers aligned head to tail. The structure implies a DNA bend of ~120°, which is in agreement with DNA bending measured in vitro. Formation of attR-containing intasomes requires only Int and Xis, distinguishing Pukovnik from lambda. Therefore, we conclude that, in Pukovnik, Xis-induced DNA bending is sufficient to promote intramolecular Int-mediated bridges during intasome formation.

Keywords: DNA bending; DNA recombination; EDTA; PEG; Xis; ethylenediaminetetraacetic acid; mycobacteriophage; polyethylene glycol; structure.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Attachment Sites, Microbiological
  • Binding Sites
  • DNA Nucleotidyltransferases / chemistry*
  • DNA Nucleotidyltransferases / metabolism*
  • DNA, Viral / chemistry*
  • DNA, Viral / metabolism*
  • Mycobacteriophages / enzymology*
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Multimerization
  • Viral Proteins / chemistry*
  • Viral Proteins / metabolism*


  • DNA, Viral
  • Viral Proteins
  • DNA Nucleotidyltransferases
  • excisionase

Associated data

  • PDB/4J2N