GMP synthetase (GMPS) catalyzes the final step of the de novo synthetic pathway of purine nucleotides. GMPS consists of two functional units which are present as domains or subunits: glutamine amidotransferase (GATase) and ATP pyrophosphatase (ATPPase). GATase hydrolyzes glutamine to yield glutamate and ammonia, while ATPPase utilizes the ammonia to convert adenyl-XMP to GMP. Here we report the crystal structure of the ATPPase subunit (PH-ATPPase) of the two-subunit-type GMPS from a hyperthermophilic archaeon Pyrococcus horikoshii OT3. PH-ATPPase consists of two domains (N- and C-domains), and exists as a homodimer in the crystal as well as in solution. The N-domain contains an ATP-binding platform called P-loop, whereas the C-domain contains the XMP-binding site and also contributes to the homodimerization. We have also demonstrated that PH-GATase alone is inactive and that all the substrates of PH-ATPPase except ammonia (Mg(2+), ATP and XMP) are required to stabilize the active complex of PH-ATPPase and PH-GATase subunits.