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Vacuolar‐type ATPases (V‐ATPases) exist in various cellular membranes of many organisms to regulate physiological processes by controlling the acidic environment. Here, we have determined the crystal structure of the A 3 B 3  subcomplex of V‐ATPase at 2.8 Å resolution. The overall construction of the A 3 B 3  subcomplex is significantly different from that of the α 3 β 3  sub‐domain in F o F 1 ‐ATP synthase, because of the presence of a protruding ‘bulge’ domain feature in the catalytic A subunits. The A 3 B 3  subcomplex structure provides the first molecular insight at the catalytic and non‐catalytic interfaces, which was not possible in the structures of the separate subunits alone. Specifically, in the non‐catalytic interface, the B subunit seems to be incapable of binding ATP, which is a marked difference from the situation indicated by the structure of the F o F 1 ‐ATP synthase. In the catalytic interface, our mutational analysis, on the basis of the A 3 B 3  structure, has highlighted the presence of a cluster composed of key hydrophobic residues, which are essential for ATP hydrolysis by V‐ATPases.

Crystal structure of A 3 B 3 complex of V‐ATPase from Thermus thermophilus