F1FO ATP Synthase

The F1FO ATP synthase is the main source of cellular ATP. It uses a transmembrane proton gradient to drive the synthesis of ATP from ADP and phosphate. The ATP synthase consists of a water-soluble F1 portion, whose crystal structure has been solved, and a transmembrane FO portion, for which little structural information exists. Proton transport through FO drives the release of ATP product on F1 by long-range conformational changes. F1 consists of five subunit types in an a3 b3g 1d1e 1 stoichiometry, with a ring of a and b subunits alternating around a single g subunit. Differential interactions of the three b subunits with the single g subunit induce asymmetry at the three catalytic sites. The catalytic sites on each of the three b subunits cycle between three binding states for substrates and products in an "alternating sites" mechanism. ATP hydrolysis has been shown to drive rotation of the g subunit within the core of F1 . During ATP synthesis, H+ translocation through FO must drive rotation of the g subunit within F1.



Three types of subunits make up FO, in an a1b2c12 stoichiometry. Low resolution images and biochemical data suggest an annular arrangement of the twelve c subunits, with subunits a and b2 on the periphery of the cylinder. The long helical subunit b dimer links subunit a of FO with the d subunit and one of the a subunits of F1. The ring of c subunits makes contact with subunit a in FO. The subunit c ring is also linked to the g subunit of the F1 core both directly, and indirectly through mutual contacts with the e subunit. An essential carboxylate, Asp61 in E. coli subunit c, translocates protons at the interface between subunits a and c. Subunit c of E. coli is a 79 residue protein that folds as two transmembrane segments connected by a polar loop. Conserved residues in the loop form part of the physical link between subunit c of FO and ge of the F1 portion of the enzyme. Current models postulate that protonation and subsequent ionization of the Asp61 side chain in subunit c lead to rotation of the c12 oligomer with respect to the a and b2 subunits. Rotation of the c12 oligomer in turn causes rotation of the e and g subunits with respect to the catalytic sites on the b subunits in F1 via the interactions between subunits c and eg. The structure of the Asp61-protonated form of subunit c at pH 5, and the structural changes within the protein induced by deprotonation of Asp61 at pH 8i have been determined. The structures of the two forms of the protein, taken together with the known interactions between subunit c monomers and between subunits a and c, suggest a mechanism for the rotation within FO that drives ATP synthesis on F1.

Conformational Changes in Subunit c During H+ Translocation:

The structures of subunit c in both protonation states share a similar helix-loop-helix topology. Comparing the two structures reveals that the main conformational change on deprotonating Asp61 is a dramatic rotation of the C-terminal helix with respect to the N-terminal helix, as can be seen by comparing the positions of labelled side chains. The N-terminal helix is virtually unaffected, with backbone RMSDs of 0.8 Å between protonated and deprotonated forms. The local geometries of the C-terminal helices are also similar in the two protonation states, with backbone atom RMSDs of 1.1 Å. But in the deprotonated form, the C-terminal helix as a unit undergoes a rotation about its axis by 140. This rotation induced by deprotonating Asp61 leads to conformational changes in the short structured loop, particularly for residues Gln42-Asp44. These residues make up most of the binding interface for the e subunit of F1.

Coordinates for Protonated Subunit c
Coordinates for Deprotonated Subunit c

Structural Model for the ac12 Oligomer


We combined the NMR structures with distance constraints derived from disulfide cross links between subunit c monomers obtained in Bob Fillingame's lab (Jones et al. 1998 J.Biol.Chem. 273, 17178), and used standard NMR structure calculation methods to calculate a family of models for the c12 oligomer which were entirely consistent with both the solution NMR data and cross-linking data from the intact complex. We then generated a family of models for the four consensus transmembrane helices of subunit a by standard NMR structure calculation methods using only published biochemical data as constraints, and positioned subunit a with respect to the c12 oligomer, using additional cysteine cross-linking data, which define the interactions between the penultimate helix of subunit a encompassing Arg210, with the C-terminal helix of the deprotonated subunit c monomer of the c12 oligomer. The final result is shown on the right.

Coordinates for ac12 complex

How it Works

Combining the structural data on protonation-linked conformational changes in subunit c with the model for the ac12 complex suggested a mechanical mechanism for proton translocation through FO and its coupling to rotation within F1, with local rotations within subunit c driving larger scale rotations of the c12 oligomer as a whole, in a "wheels within wheels" type of mechanism. The mechanism is outlined briefly below.

Links to ATP Synthase Movies (most from other labs):

Animation of ATP Synthase in Action (W. Junge Lab)

Animation of Fo Rotation (Girvin Lab)

Direct Visualization of Rotation by F1 (Noji, Yoshida, et al.)

Mechanics and Mechanisms of F1FO ATP Synthase (G. Oster Lab)


V.K. Rastogi & M.E. Girvin (1999) Structural changes linked to proton translocation by subunit c of the ATP Synthase, Nature 402:263. (Abstract)

V.K. Rastogi & M.E. Girvin (1999) 1H, 13C, 15N Assignments and Secondary Structure of the High pH Form of Subunit c of the F1FO ATP Synthase, J. Biomolecular NMR 13:91.

M.E. Girvin, V.K. Rastogi, F. Abildgaard, J.L. Markley & R.H. Fillingame (1998) Solution Structure of the Transmembrane H+-Translocating Subunit c of the F1FO ATP Synthase, Biochemistry 37:8817. (Abstract)

M.E. Girvin & R.H. Fillingame (1995) Determination of Local Protein Structure by Spin Label Difference 2D NMR, Biochemistry 34:1635. (Abstract)

Supported by: National Institutes of Health & National Science Foundation

Last revised: November 19, 1999