Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases

V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with F(o)F(1) ATP synthase. When powered by ATP hydrolysis, the V(1) domain rotates the central rotor against the A(3)B(3) hexamer, composed of three catalytic AB dimers adopting different conformations (AB(open), AB(semi), and AB(closed)). Here, we report the atomic models of 18 catalytic intermediates of the V(1) domain of V/A-ATPase under different reaction conditions, determined by single particle cryo-EM. The models reveal that the rotor does not rotate immediately after binding of ATP to the V(1). Instead, three events proceed simultaneously with the 120˚ rotation of the shaft: hydrolysis of ATP in AB(semi), zipper movement in AB(open) by the binding ATP, and unzipper movement in AB(closed) with release of both ADP and Pi. This indicates the unidirectional rotation of V/A-ATPase by a ratchet-like mechanism owing to ATP hydrolysis in AB(semi), rather than the power stroke model proposed previously for F(1)-ATPase.