Endonuclease which cleaves flap structures at the junction between single-stranded DNA and double-stranded DNA with a specific cleavage site in the 5' overhang strand exactly one nucleotide 3' of the branch point (PubMed:25037209). Structure- and sequence-specific nuclease that resolves holliday junctions (HJs) by symmetrically oriented incisions in two opposing strands near the junction point, thus leading to ligatable products; HJs are physical links between homologous DNA molecules that arise as central intermediary structures during homologous recombination and repair in meiotic and somatic cells (PubMed:25037209). Structure-specific nuclease with 5'-flap endonuclease activity, preferentially cleaving static flaps 5' overhang strand exactly one nucleotide in the 3' direction of the branch point (PubMed:25037209). Also able to cleave double-stranded flap strand 1 exactly at the branch point (PubMed:25037209). Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding. A number of isoforms are produced. According to EST sequences. Normal sensitivity to DNA damaging agents (PubMed:26704385). Mild UV sensitivity in the gen1 send1 double mutant (PubMed:26704385). Belongs to the XPG/RAD2 endonuclease family. GEN subfamily.