Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 Å resolution

The structure of the intact ATP synthase from the alpha-proteobacterium Paracoccus denitrificans, inhibited by its natural regulatory zeta-protein, has been solved by X-ray crystallography at 4.0 angstrom resolution. The zeta-protein is bound via its N-terminal alpha-helix in a catalytic interface in the F-1 domain. The bacterial F-1 domain is attached to the membrane domain by peripheral and central stalks. The delta-subunit component of the peripheral stalk binds to the N-terminal regions of two alpha-subunits. The stalk extends via two parallel long a-helices, one in each of the related b and b' subunits, down a noncatalytic interface of the F-1 domain and interacts in an unspecified way with the a-subunit in the membrane domain. The a-subunit lies close to a ring of 12 c-subunits attached to the central stalk in the F-1 domain, and, together, the central stalk and c-ring form the enzyme's rotor. Rotation is driven by the transmembrane proton-motive force, by a mechanism where protons pass through the interface between the a-subunit and c-ring via two half-channels in the a-subunit. These half-channels are probably located in a bundle of four a-helices in the a-subunit that are tilted at similar to 30 degrees to the plane of the membrane. Conserved polar residues in the two a-helices closest to the c-ring probably line the proton inlet path to an essential carboxyl group in the c-subunit in the proton uptake site and a proton exit path from the proton release site. The structure has provided deep insights into the workings of this extraordinary molecular machine.