The Cre recombinase cleaves the lox site in trans.

The Cre protein is a conservative site-specific recombinase that is encoded by bacteriophage P1. Its function in vivo is to resolve dimeric lysogenic P1 plasmids that arise by general recombination. In this way Cre facilitates effective partition of the P1 prophage. Cre is a member of the integrase family of conservative site-specific recombinases. Cleavage of the DNA by the integrases involves covalent attachment of a conserved nucleophilic tyrosine to the 3'-phosphoryl end at the site of the break. We have used in vitro complementation tests to show that the Cre protein, like the Flp protein of the 2-microm plasmid of Saccharomyces cerevisiae, cleaves its target lox site in trans. Moreover, the data are compatible with two modes of cleavage; one requires the reconstitution of a pseudo full-site from half-sites and the other requires the assembly of a higher order complex that resembles a synaptic complex.