Catalyzes the phosphorylation of pantothenate the first step in CoA biosynthesis. May play a role in the physiological regulation of the intracellular CoA concentration. Functionally redudant with PANK1 (By similarity). The phosphatase activity shows preference for normal or oxidatively damaged intermediates of 4'-phosphopantetheine, which provides strong indirect evidence that the phosphatase activity pre-empts damage in the CoA pathway (By similarity). Hydrolyzing excess 4'-phosphopantetheine could constitute a directed overflow mechanism to prevent its oxidation to the S-sulfonate, sulfonate, or other forms (By similarity). Hydrolyzing 4'-phosphopantetheine sulfonate or S-sulfonate would forestall their conversion to inactive forms of CoA and acyl carrier protein (By similarity). (R)-pantothenate + ATP = (R)-4'-phosphopantothenate + ADP + H(+) (R)-4'-phosphopantothenate + H2O = (R)-pantothenate + phosphate (R)-4'-phosphopantetheine + H2O = (R)-pantetheine + phosphate (R)-4'-phosphopantetheine sulfonate + H2O = (R)-pantetheine sulfonate + phosphate Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-pantothenate: step 1/5. Subfamily II proteins have an EGMGR motif about 50 residues from the C-terminus (By similarity). This motif lies near the metal-binding residues in the putative substrate-binding cleft 2 (By similarity). Subfamily II proteins occur only in eukaryotes, in two forms: as a stand-alone unit in plants, and as a C-terminal domain of pantothenate kinases in plants, animals, and chytrid fungi (By similarity). In the N-terminal section; belongs to the type II pantothenate kinase family. In the C-terminal section; belongs to the damage-control phosphatase family. Phosphopantetheine phosphatase II subfamily.