Structural analysis of the RuvC-Holliday junction complex reveals an unfolded junction

The RuvC protein of Escherichia coli is an endonuclease that specifically recognises and cleaves Holliday junctions during genetic recombination. The structure of the RuvC-Holliday junctions complex has been investigated by DNAse I footprinting and by gel electrophoretic analysis. We find that RuvC binds to the Holliday junction to form a complex that exhibits 2-fold symmetry, and in which the three-dimensional structure of the Holliday junction is altered to an unfolded form. This structure is observed in the absence or presence of divalent metal ions and differs from either the unfolded square or the folded stacked X-structures that have been observed with protein-free Holliday junctions. KMnO4 was used to probe the junction DNA upon binding by RuvC, and indicates that base-pairing at the crossover is disrupted within the RuvC-Holliday junction.