Cre recombinase catalyzes site-specific recombination between 34-bp loxP sites in a variety of topological and cellular contexts. An obligatory step in the recombination reaction is the association, or synapsis, of Cre-bound loxP sites to form a tetrameric protein assembly that is competent for strand exchange. Using analytical ultracentrifugation and electrophoresis approaches, we have studied the energetics of Cre-mediated synapsis of loxP sites. We found that synapsis occurs with a high affinity (K d ‫؍‬ 10 nM) and is pH-dependent but does not require divalent cations. Surprisingly, the catalytically inactive Cre K201A mutant is fully competent for synapsis of loxP sites, yet the inactive Y324F and R173K mutants are defective for synapsis. These findings have allowed us to determine the first crystal structures of a pre-cleavage Cre-loxP synaptic complex in a configuration representing the starting point in the recombination pathway. When combined with a quantitative analysis of synapsis using loxP mutants, the structures explain how the central 8 bp of the loxP site are able to dictate the order of strand exchange in the Cre system.Site-specific recombinases from the tyrosine recombinase family are used by bacteria and yeast to mediate the integration, excision, resolution, and inversion of DNA segments to carry out a wide variety of biological functions (1, 2). In the simplest systems, typified by the bacteriophage P1 Cre recombinase (3) and the Saccharomyces cerevisiae Flp recombinase (4), only the recombinase enzymes and DNA substrates containing 34-bp recombination sequences are required for efficient recombination. In others, such as the bacteriophage -integrase (-int) 3 (5) and the Escherichia coli XerC and XerD recombinases (6), efficient recombination requires more complex recombination sites and the activities of auxiliary proteins that tightly regulate the forward and reverse reactions. A remarkable property of both the simple and complex systems is their ability to efficiently synapse (associate) recombining sites that can be located far from one another on the same chromosome or, for bacteriophage integration, are in separate DNA molecules.Synapsis of recombining sites has been visualized in tyrosine recombinase systems using a variety of complementary experimental approaches. For example, synaptic -int att and CreloxP complexes have been observed by electron microscopy (7, 8) and as slower-migrating bands on non-denaturing polyacrylamide gels (9,10

Members of the tyrosine recombinase (YR) family of site-specific recombinases catalyze DNA rearrangements using phosphoryl transfer chemistry that is identical to that used by the type IB topoisomerases (TopIBs). To better understand the requirements for YR catalysis and the relationship between the YRs and the TopIBs, we have analyzed the in vivo and in vitro recombination activities of all substitutions of the seven active site residues in Cre recombinase. We have also determined the structure of a vanadate transition state mimic for the Cre–loxP reaction that facilitates interpretation of mutant activities and allows for a comparison with similar structures from the related topoisomerases. We find that active site residues shared by the TopIBs are most sensitive to substitution. Only two, the tyrosine nucleophile and a conserved lysine residue that activates the 5′-hydroxyl leaving group, are strictly required to achieve >5% of wild-type activity. The two conserved arginine residues each tolerate one substitution that results in modest recombination activity and the remaining three active site positions can be substituted with several alternative amino acids while retaining a significant amount of activity. The results are discussed in the context of YR and TopIB structural models and data from related YR systems.

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