Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate. Phosphatase that hydrolyzes non-canonical purine nucleotides such as XTP and ITP to their respective diphosphate derivatives. Probably excludes non-canonical purines from DNA/RNA precursor pool, thus preventing their incorporation into DNA/RNA and avoiding chromosomal lesions. (R)-4'-phosphopantetheine + ATP + H(+) = 3'-dephospho-CoA + diphosphate H2O + XTP = H(+) + phosphate + XDP H2O + ITP = H(+) + IDP + phosphate Binds 1 divalent metal cation per subunit; can use either Mg(2+) or Mn(2+). Cofactor biosynthesis; coenzyme A biosynthesis. In the N-terminal section; belongs to the eukaryotic CoaD family. In the C-terminal section; belongs to the YjjX NTPase family.