Serine/threonine protein kinase which activates checkpoint signaling upon genotoxic stresses such as ionizing radiation (IR) or DNA replication stalling. Plays a central role in the perception and response to both stress-induced damage in somatic cells and developmentally programmed DNA damage during meiosis. Recognizes the substrate consensus sequence [ST]-Q. Phosphorylates histone variant H2AX to form H2AXS139ph at double strand breaks (DSBs), thereby regulating DNA damage response mechanism. Involved in transcriptional regulation of RAD51, PARP1, GR1, and LIG4 in response to DNA double strand breaks. Plays a dual role by activating the DNA damage response at dysfunctional telomeres and yet preventing this activation at functional telomeres. Not required for telomere length homeostasis. Regulates DNA damage response (DDR) synergistically with RUG3. Together with RUG3, involved in the splicing of the ND2/NAD2 mRNA (PubMed:28262819). ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Interacts with RUG3. Ubiquitously expressed at low levels with slightly higher levels in flower buds. Plants show meiotic defects, hypersensitivity to double strand breaks-inducing agents, and an inability to properly induce IR-mediated transcription of several DNA repair genes. Augmented DNA damage response (DDR) associated with increased intracellular reactive oxygen species (ROS) levels in response to methyl methanesulfonate (MMS) treatment (PubMed:28262819). Belongs to the PI3/PI4-kinase family.