Switching catalytic activity in the XerCD site-specific recombination machine

The tyrosine family site-specific recombinases, XerCD, function in the conversion of circular dimer replicons to monomers. In the recombining complex that contains two synapsed recombination sites and two molecules each of XerC and XerD, the DNA strand-exchange reactions are separated in time and space. XerC initiates recombination to form a Holliday junction intermediate, which undergoes a conformational change to provide a substrate for strand exchange by XerD. XerCD are two-domain proteins, whose C-terminal domains contain all of the catalytic residues. We show that XerC or XerD variants lacking their N-terminal domains are active in recombination when combined with their wild-type partner. Nevertheless, the normal pattern of catalysis is dramatically altered; strand exchange by the recombinase variant is stimulated, while that by the wild-type partner recombinase is impaired. The primary determinants for the mutant phenotype reside in the region of α-helix B of XerD. We propose that altered interactions within the recombining heterotetramer lead to changes in the relative concentrations of the two alternative Holliday junction substrates that are recombined by XerC or XerD, respectively.