The strict anaerobic bacterium Propionigenium modestum performs a Na+ cycle over the membrane to couple ATP synthesis to the decarboxylation of methyl-malonyl-CoA. The responsible ATPase has a typical F1F0 structure, the water-soluble F1 moiety being composed of five different subunits and the more firmly membrane-bound F0 part consisting of three different subunits. The F1F0 ATPase but not F1 alone was specifically activated by Na+ ions, suggesting that the Na+ binding site is located on the F0 moiety. The ATPase reconstituted into proteoliposomes catalyzed an ATP-dependent Na+ accumulation that was stimulated to the same extent by dissipating the membrane potential with valinomycin or with the uncoupler carbonylcyanide-m-chloro phenylhydrazone. The transport of Na+ is therefore a primary event, not a secondary event involving the intermediate formation of a proton gradient. The ATPase also catalyzed H+ translocation at Na+ concentrations below 1 mM. Our results indicate a common mechanism of the ATPase for Na+ and H+ (H3O+) translocation and a switch from H+ to Na+ translocation by increasing the Na+ concentration. A hybrid ATPase consisting of F1 from E. coli and F0 from P. modestum had the same specificity with respect to the translocated cations as the homologous F1F0 ATPase of P. modestum, indicating again that the Na+ (H+) binding site is located on the F0 part. Also in accord with this supposition is a diffusion potential-induced translocation of Na+ or H+ through the F0 part of the enzyme complex. The phylogenetic relationship between the Na(+)-translocating ATPase of P. modestum and other F1F0 ATPases has been clearly demonstrated by sequencing studies.