ATP synthases are the primary source of ATP in all living cells. To catalyze ATP synthesis, these membrane-associated complexes use a rotary mechanism powered by the transmembrane diffusion of ions down a concentration gradient. ATP synthases are assumed to be driven either by H + or Na + , reflecting distinct structural motifs in their membrane domains, and distinct metabolisms of the host organisms. Here, we study the methanogenic archaeon Methanosarcina acetivorans using assays of ATP hydrolysis and ion transport in inverted membrane vesicles, and experimentally demonstrate that the rotary mechanism of its ATP synthase is coupled to the concurrent translocation of both H + and Na + across the membrane under physiological conditions. Using free-energy molecular simulations, we explain this unprecedented observation in terms of the ion selectivity of the binding sites in the membrane rotor, which appears to have been tuned via amino acid substitutions so that ATP synthesis in M. acetivorans can be driven by the H + and Na + gradients resulting from methanogenesis. We propose that this promiscuity is a molecular mechanism of adaptation to life at the thermodynamic limit.F rom archaea to man, the common enzyme in cellular bioenergetics is the ATP synthase. This membrane-bound macromolecular complex produces ATP, the primary energy source in the cell, at the expense of transmembrane ion gradients established by diverse enzymes, which vary across organisms and organelles. ATP synthases and related ATPases arose from a common ancestor and evolved into three distinct classes: the V 1 V 0 ATPase present in eukarya; the F 1 F 0 ATP synthase found in bacteria, mitochondria, and chloroplasts; and the A 1 A 0 ATP synthase present in archaea (1, 2). All of these synthases are rotary machines that comprise two coupled units, one residing in the cytoplasm (F 1 /A 1 /V 1 ), and another (F o /A o /V o ) embedded in the membrane. The former catalyzes ATP synthesis (or hydrolysis), and the latter is coupled to the transmembrane electrochemical potential (3)(4)(5)(6)(7)(8).The ion specificity of ATP synthases/ATPases is encoded by the membrane-embedded domain, and in particular in the rotor ring. This ring is an oligomeric assembly of multiple copies of subunit c, each of which carries at least one ion binding site. The architecture of the membrane domain enables the rotation of the c ring around its central axis in a manner that is tightly coupled to ion flow across the membrane (9-12). The rotation of the c ring is also mechanically transmitted to the cytoplasmic domain, where it sustains a conformational cycle conducive to ATP synthesis (13,14).Most F 1 F 0 ATP synthases and V 1 V 0 ATPases use protons as the coupling ion, but some use sodium ions instead (15-17). However, Na + -driven F 1 F 0 ATP synthases have so far been found only in anaerobic bacteria, whose metabolism leads to the generation of a primary Na + gradient, rather than a H + gradient (16,17). Na + is clearly preferred over H + in these ATP synthases (18,19). ...