The archaeal ATPase of the halophile Haloferax volcanii synthesizes ATP at the expense of a proton gradient, as shown by sensitivity to the uncoupler carboxyl cyanide p-trifluoromethoxyphenylhydrazone, to the ionophore nigericin, and to the proton channel-modifying reagent N,N-dicyclohexylcarbodiimide. The conditions for an optimally active ATP synthase have been determined. We were able to purify the enzyme complex and to identify the larger subunits with antisera raised against synthetic peptides. To identify additional subunits of this enzyme complex, we cloned and sequenced a gene cluster encoding five hydrophilic subunits of the A 1 part of the proton-translocating archaeal ATP synthase. Initiation, termination, and ribosome-binding sequences as well as the result of a single transcript suggest that the ATPase genes are organized in an operon. The calculated molecular masses of the deduced gene products are 22.0 kDa (subunit D), 38.7 kDa (subunit C), 11.6 kDa (subunit E), 52.0 kDa (subunit B), and 64.5 kDa (subunit A). The described operon contains genes in the order D, C, E, B, and A; it contains no gene for the hydrophobic, so-called proteolipid (subunit c, the proton-conducting subunit of the A 0 part). This subunit has been isolated and purified; its molecular mass as deduced by SDS-polyacrylamide gel electrophoresis is 9.7 kDa.The archaeon (archaebacterium) Haloferax volcanii belongs to the more moderate halophilic archaea, growing best in a medium containing 2 mol/liter NaCl and 0.25 mol/liter MgCl 2 at pH 7 (1). The proton-conducting ATPase of this archaeon is a halophilic enzyme that shows maximum activity at 1.75 mol/liter NaCl. It was characterized recently with respect to its hydrolytic function (2). The membrane-bound ATPases from archaea share properties with both bacterial (formerly eubacterial) and eucaryal (formerly eukaryotic) ATPases. Like F 0 F 1 -ATPases, they are able to synthesize ATP from ADP and phosphate coupled to a proton flow. Genetically derived amino acid sequences of the large subunits of archaeal ATPases (2-6), immunological cross-reactivity (7,8), and inhibition of the enzymes by specific inhibitors (1, 9 -11) deliver the main arguments for the conclusion that the archaeal ATPases resemble eucaryal vacuolar ATPases (V-ATPases) 1 more closely than bacterial F-ATPases.The primary structures of subunits A and B of H. volcanii are closely related to those of Halobacterium salinarium (halobium) (6) and indeed more related to the class of the eucaryal V-ATPases. On the other hand, the function of eucaryal VATPases is to generate a ⌬ H ϩ at the expense of ATP hydrolysis; they are not able to synthesize ATP in a reversed reaction. More detailed investigations on the intermediate position of different archaeal ATPases are required.Up to now, almost nothing was known about the small subunits of halophilic ATPases. F-ATPases have one copy each of three different small subunits, ␥, ␦, and ⑀, which are involved in proton conduction and/or regulation (for review, see Refs. 12 and 13). V-A...