Required for the final endonucleolytic cleavage at site D converting 20S pre-rRNA into the mature 18S rRNA. Required for the final steps of cytoplasmic maturation of the 40S ribosomal subunit. The association with the very late 40S subunit intermediate seems to follow RIO2 association with precursors of the 40S subunit and may involve a translation-like checkpoint point cycle preceeding the binding to the 60S ribosomal subunit. Despite the protein kinase domain is proposed to act predominantly as an ATPase. The catalytic activity regulates its dynamic association with the 40S subunit. Has a role in the cell cycle where it is required for entrance into S-phase and in the control of the onset of anaphase. Appears to also be involved in the maintenance of chromosome stability and correct mitotic segregation. ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein] ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein] Can use both Mg(2+) and Mn(2+) in vitro and shows higher activity with Mn(2+) but Mg(2+) is likely to be the in vivo cofactor. Interacts with CKA2. Autophosphorylated. Phosphorylated by casein kinase II (CK2). Phosphorylation by CK2 stimulates RIO1 kinase activity and targets it for degradation at the G1/S transition of the cell cycle. Belongs to the protein kinase superfamily. RIO-type Ser/Thr kinase family.