A conserved nuclease domain in the archaeal Holliday junction resolving enzyme Hjc

Holliday junction resolving enzymes are ubiquitous proteins that function i n the pathway of homologous recombination, catalyzing the rearrangement and repair of DNA. They are metal ion-dependent endonucleases with strong stru ctural specificity for branched DNA species. Whereas the eukaryotic nuclear enzyme remains unknown, an archaeal Holliday junction resolving enzyme, Hj c, has recently been identified. We demonstrate that Hjc manipulates the gl obal structure of the Holliday junction into a 2-fold symmetric X shape, wi th local disruption of base pairing around the point of cleavage that occur s in a region of duplex DNA 3' to the point of strand exchange. Primary and secondary structural analysis reveals the presence of a conserved catalyti c metal ion binding domain in Hjc that has been identified previously in se veral restriction enzymes. The roles of catalytic residues conserved within this domain have been confirmed by site-directed mutagenesis, This is the first example of this domain in an archaeal enzyme of known function as wel l as the first in a Holliday junction resolving enzyme.