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Structure of the Holliday junction intermediate in Cre–loxP site‐specific recombination

We have determined the X‐ray crystal structures of two DNA Holliday junctions (HJs) bound by Cre recombinase. The HJ is a four‐way branched structure that occurs as an intermediate in genetic recombination pathways, including site‐specific recombination by the λ‐integrase family. Cre recombinase is an integrase family member that recombines 34 bp loxP sites in the absence of accessory proteins or auxiliary DNA sequences. The 2.7 Å structure of Cre recombinase bound to an immobile HJ and the 2.5 Å structure of Cre recombinase bound to a symmetric, nicked HJ reveal a nearly planar, twofold‐symmetric DNA intermediate that shares features with both the stacked‐X and the square conformations of the HJ that exist in the unbound state. The structures support a protein‐mediated crossover isomerization of the junction that acts as the switch responsible for activation and deactivation of recombinase active sites. In this model, a subtle isomerization of the Cre recombinase–HJ quaternary structure dictates which strands are cleaved during resolution of the junction via a mechanism that involves neither branch migration nor helical restacking.