Catalyzes the hydrolysis of phosphoanhydride bonds of nucleoside tri- and di-phosphates. Has equal high activity toward ADP/ATP, GDP/GTP, and UDP/UTP and approximately 50% less toward CDP/CTP and thiamine pyrophosphate. Has no activity toward GMP. Required for Golgi glycosylation and cell wall integrity. Together with CDC55, required for adenovirus E4orf4 (early region 4 open reading frame 4) induced toxicity, the apyrase activity is not required for this function. Plays a role in sphingolipid synthesis. a ribonucleoside 5'-triphosphate + 2 H2O = a ribonucleoside 5'-phosphate + 2 H(+) + 2 phosphate A divalent cation Ca(2+), Mg(2+) or Mn(2+). Activity is inhibited both by interaction with VMA13 and by V-ATPase acidification of the lumen. The activity of VMA13 is not required for YND1 inhibition. Protein modification; protein glycosylation. Interacts with activator subunit VMA13 of vacuolar H(+)-ATPase. Interacts with CDC55; this interaction is disrupted by adenovirus E4orf4, which remains associated with both YND1 and CDC55. Cells are partially resistant to E4orf4 and can partially suppress the spindle checkpoint defect in CDC55 deletion mutant. Does not suppress the rapamycin-resistance of CDC55 deletion mutant. YND1 and CDC55 double mutant is fully resistant to E4orf4. Deletion mutant suppresses the synthetic lethality of triple mutants, where UPC2 and ECM22 are knocked out along with either HAP1, ERG6 or ERG28. Present with 450 molecules/cell in log phase SD medium. Belongs to the GDA1/CD39 NTPase family.