5DN6

ATP synthase from Paracoccus denitrificans

Summary for 5DN6

• Entry DOI: 10.2210/pdb5dn6/pdb
• Related: 2XND 2XOK 5CDF
• Descriptor: Chain A, Chain V, Chain W, ... (17 entities in total)
• Functional Keywords: hydrolase, paracoccus denitrificans, atp synthase, complex, regulation, proton translocation
• Biological source: Paracoccus denitrificans; More
• Total number of polymer chains: 29
• Total formula weight: 545795.14

Authors

Morales-Rios, E.,Montgomery, M.G.,Leslie, A.G.W.,Walker, J.E. (deposition date: 2015-09-09, release date: 2015-10-28, Last modification date: 2024-05-08)

Primary citation

Morales-Rios, E.,Montgomery, M.G.,Leslie, A.G.,Walker, J.E.
Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 angstrom resolution.
Proc.Natl.Acad.Sci.USA, 112:13231-13236, 2015

PubMed Abstract: The structure of the intact ATP synthase from the α-proteobacterium Paracoccus denitrificans, inhibited by its natural regulatory ζ-protein, has been solved by X-ray crystallography at 4.0 Å resolution. The ζ-protein is bound via its N-terminal α-helix in a catalytic interface in the F1 domain. The bacterial F1 domain is attached to the membrane domain by peripheral and central stalks. The δ-subunit component of the peripheral stalk binds to the N-terminal regions of two α-subunits. The stalk extends via two parallel long α-helices, one in each of the related b and b' subunits, down a noncatalytic interface of the F1 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 F1 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 α-helices in the a-subunit that are tilted at ∼30° to the plane of the membrane. Conserved polar residues in the two α-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.

PubMed: 26460036
DOI: 10.1073/pnas.1517542112

Experimental method

X-RAY DIFFRACTION (3.98 Å)