RuvC is the endonuclease that cleaves the Holliday junctions (Figure 8.20). It forms dimers that bind to the Holliday junction; recent data indicate an interaction among RuvA, RuvB and RuvC as a complex at the Holliday junction. The structure of the RuvA-Holliday junction complex (Figure 8.18) suggests that the open structure of the junction stabilized by the binding of RuvA may expose a surface that is recognized by Ruv C for cleavage. RuvC cleaves symmetrically, in two strands with the same nearly identical sequences, thereby producing ligatable products.
The preferred site of cleavage by RuvC is 5’ WTT’S, where W = A or T and S = G or C, and ‘ is the site of cleavage. RuvC can cut strands for either horizontal or vertical resolution. Strand choice is influenced by the sequence preference and also by the presence of RecA protein, which favors vertical cleavage (i.e. to cause recombination of flanking markers).