Vacuolar proton-translocating ATPase pumps consist of two domains, V 1 and V o . Subunit d is a component of V o located in a central stalk that rotates during catalysis. By generating mutations, we showed that subunit d couples ATP hydrolysis and proton transport. The mutation F94A strongly uncoupled the enzyme, preventing proton transport but not ATPase activity. C-terminal mutations changed coupling as well; ATPase activity was decreased by 59 -72%, whereas proton transport was not measurable (E328A) or was moderately reduced (E317A and C329A). Except for W325A, which had low levels of V 1 V o , mutations allowed wild-type assembly regardless of the fact that subunits E and d were reduced at the membrane. N-and C-terminal deletions of various lengths were inhibitory and gradually desta- Viral infections, cancer, osteoporosis, and renal tubular acidosis are some of the human disease states associated with the V-ATPase 2 function. V-ATPases are ATP-driven proton pumps present in Golgi, endosomes, lysosomes, and vacuoles, where they are responsible for maintaining the acidic luminal pH essential for receptor-mediated endocytosis, zymogen activation, and protein sorting (1-4). In addition to the endogenously distributed V-ATPases, some cells contain V-ATPases at the plasma membrane, where they pump protons from the cytosol to the extracellular milieu. V-ATPase proton transport across the plasma membrane is essential for bone resorption, urinary acidification, sperm maturation, and neurotransmitter sequestration (3).V-ATPases are related to F-ATP synthases (5), and both protein complexes work as molecular motors (6 -9). V-ATPases, however, work exclusively in the direction of ATP hydrolysis in vivo. V-ATPases consist of two domains, V 1 and V o , similar to the F 1 and F o domains found in ATP synthases (1-4). Eight different subunits (A-H) compose V 1 , which is peripherally attached to the membrane and hydrolyzes ATP (1-4). Six different subunits (a, c, cЈ, cЉ, d, and e) associate to form V o , which holds V 1 at the membrane and forms the path to transport protons (1-4). V 1 and V o subunits contribute to the formation of one central stalk and two or three peripheral stalk structures that connect a proteolipid ring (made of subunits c, cЈ, and cЉ) in V o and the catalytic core of V 1 (a hexamer of three subunits A alternating with three subunits B) (10, 11).The organization of the central and peripheral stalks is essential for structural and functional coupling of ATP hydrolysis and proton transport. It is proposed that during catalysis, ATP hydrolysis at the V 1 hexamer A 3 B 3 drives rotation of a rotor (central stalk made of subunits D, F, and d connected to the proteolipid ring) (6, 12). Six essential glutamates are protonated in the ring when protons are transferred from the cytosol via two half-tunnel structures formed in the stationary subunit a at the membrane (13-15). By connecting the stationary subunits (A 3 B 3 and a), the peripheral stalk(s) (subunits C, E, G, H, and the N terminus of subunit a) wo...