Single-stranded DNA endonuclease activity in vitro (PubMed:12602891). May not be active as double-stranded DNA endonuclease (PubMed:12602891). 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 (By similarity). 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 (By similarity). Probably involved in the resolution of toxic replication structures to ensure genome stability, and to maintain telomere integrity and replication (By similarity). 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. Highly expressed in shoot apical meristem (SAM) and young leaves. Expressed in roots, flag leaf and panicles. By the DNA-damaging agents methyl methanesulfonate (MMS), H(2)O(2) and UV. Down-regulated by sucrose starvation and the cell cycle inhibitors aphidicolin, hydroxyurea and colchicine. Belongs to the XPG/RAD2 endonuclease family. GEN subfamily.