Endonuclease which resolves Holliday junctions (HJs) by the introduction of symmetrically related cuts across the junction point, to produce nicked duplex products in which the nicks can be readily ligated. Four-way DNA intermediates, also known as Holliday junctions, are formed during homologous recombination and DNA repair, and their resolution is necessary for proper chromosome segregation (PubMed:19020614, PubMed:26682650). Cleaves HJs by a nick and counter- nick mechanism involving dual coordinated incisions that lead to the formation of ligatable nicked duplex products. Cleavage of the first strand is rate limiting, while second strand cleavage is rapid. Largely monomeric, dimerizes on the HJ and the first nick occurs upon dimerization at the junction (PubMed:26578604). Efficiently cleaves both single and double HJs contained within large recombination intermediates. Exhibits a weak sequence preference for incision between two G residues that reside in a T-rich region of DNA (PubMed:28049850). Also has endonuclease activity on 5'-flap and replication fork (RF) DNA substrates (PubMed:26578604). {ECO:0000269|PubMed:19020614, ECO:0000269|PubMed:26578604, ECO:0000269|PubMed:26682650, ECO:0000269|PubMed:28049850}. This is the function of GEN1 (GEN1 structure-specific endonuclease, ENSG00000178295).