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

• Published in: Journal of molecular biology 2014-01, Vol.426 (2), p.412-422
• Main Authors: Singh, Shweta, Plaks, Joseph G., Homa, Nicholas J., Amrich, Christopher G., Héroux, Annie, Hatfull, Graham F., VanDemark, Andrew P.
• Format: Article
• Language: English
• Subjects: Attachment Sites, Microbiological; Binding Sites; DNA bending; DNA Nucleotidyltransferases - chemistry; DNA Nucleotidyltransferases - metabolism; DNA recombination; DNA, Viral - chemistry; DNA, Viral - metabolism; mycobacteriophage; Mycobacteriophages - enzymology; Protein Binding; Protein Interaction Domains and Motifs; Protein Multimerization; structure; Viral Proteins - chemistry; Viral Proteins - metabolism; Xis
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2013.10.002

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. [Display omitted] •Mycobacteriophage Pukovnik can support excision in the absence of mIHF.•Helical Pukovnik Xis filaments contain canonical and domain-swapped protomers.•Xis introduces a 106° bend in attR DNA consistent with the filament structure.•The highly bent filament constrains intasome architecture to enforce directionality.