An archaeal Holliday junction resolving enzyme from Sulfolobus solfataricus exhibits unique properties

The rearrangement and repair of DNA by homologous recombination often invol ves the creation of Holliday junctions, which must be cleaved by junction-s pecific endonucleases to yield recombinant duplex DNA products. Holliday ju nction resolving enzymes are a ubiquitous class of proteins with diverse st ructural and mechanistic characteristics. We have characterised an endonucl ease (Hje) from the thermophilic crenarchaeote Sulfolobus solfataricus that exhibits a high degree of specificity for Holliday junctions via an appare ntly novel mechanism. Hje resolves four-way DNA junctions by the introducti on of paired nicks in a reaction that is independent of the local nucleotid e sequence, but is restricted solely to strands that are continuous in the stacked-X form of the junction. Three-way DNA junctions are cleaved only wh en the presence of a bulge in one strand allows the junction to stack in an analogous manner to four-way junctions. These properties differentiate Hje from all other known junction resolving enzymes. (C) 2000 Academic Press.