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Background  The  Gifsy-1  phage integrates into the  Salmonella  Typhimurium chromosome via an integrase mediated, site-specific recombination mechanism. Excision of the  Gifsy-1  phage requires three proteins, the  Gifsy-1  integrase (Int), the  Gifsy-1  excisionase (Xis) protein, and host encoded Integration Host Factor (IHF). The  Gifsy-1 xis  gene encodes the 94-residue  Gifsy-1  excisionase protein that has a molecular weight of 11.2 kDa and a pI of 10.2. Electrophoretic Mobility Shift Assays (EMSA) suggested at least one region of the protein is responsible for protein-DNA interactions with a tripartite DNA binding site composed of three direct imperfect repeats.    Results  Here we have undertaken experiments to dissect and model the structural motifs of  Gifsy-1  Xis necessary for its observed DNA binding activity. Diethyl sulfate mutagenesis (DES) and mutagenic PCR techniques were used to generate  Gifsy-1 xis  mutants. Mutant Xis proteins that lacked activity in vivo were purified and tested by EMSA for binding to the  Gifsy-1  Xis  attP  attachment site. Results from mutagenesis experiments and EMSA were compared to results of structural predictions and sequence analyses.    Conclusion  Sequence comparisons revealed evidence for three distinct structural motifs in the  Gifsy-1  Xis protein. Multiple sequence alignments revealed unexpected homologies between the  Gifsy-1  Xis protein and two distinct subsets of polynucleotide binding proteins. Our data may suggest a role for the  Gifsy-1  Xis in the regulation of the  Gifsy-1  phage excision beyond that of DNA binding and possible interactions with the  Gifsy-1  Int protein.

Structural Prediction and Mutational Analysis of the Gifsy-1 Xis Protein