Involved in the dephosphorylation and activation of the transcription factor GLN3 in response to nutrient availability. Forms the histone H2A phosphatase complex in association with the regulatory subunits PSY2 and PSY4, which dephosphorylates H2AS128ph (gamma-H2A) that has been displaced from sites of DNA lesions in the double-stranded DNA break repair process. Dephosphorylation is necessary for efficient recovery from the DNA damage checkpoint (By similarity). H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] + phosphate H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate Binds 2 manganese ions per subunit. Catalytic subunit of the histone H2A phosphatase complex (HTP-C) containing PPH3, PSY2 and PSY4. Belongs to the PPP phosphatase family. PP-4 (PP-X) subfamily.