Subunit composition of the ATP synthase
There are minor differences between bacteria, mitochondria and chloroplasts in some of the smaller subunits, which leads to a confusing nomenclature. The simplest system is that from E. coli. The ATP synthase can be dissociated into two fractions by relatively mild salt treatments.
A soluble portion, the F1 ATP-ase, contains 5 subunits, in a stoichiometry of 3a:3b:1g:1d:1e. Three substrate binding sites are in the b-subunits. Additional adenine nucleotide binding site in the a-subunits are regulatory. The F1 portion catalyzes ATP hydrolysis, but not ATP-synthesis.
Dissociation of the the F1 ATP-ase from the membranes of bacteria or organelles leaves behind a membrane embedded portion called FO. This consists (in E. coli) of three subunits a, b and c, with relative stoichiometries of 1:2:9-12. The c-subunit is very hydrophobic, and forms a helix turn helix structure which spans the membrane twice, with a hydrophilic loop on the side of attachment of F1. There is a conserved acidic residue half-way across the membrane in the C-terminal helix.
After dissociation, the membranes are permeable to protons. The proton leak can be stopped by addition of inhibitors, which are also inhibitors of ATP synthesis in the functional complex. Two "classical" inhibtors are commonly used. Oligomycin binds at the interface between Fo and F1; dicyclohexylcarbodiimide (DCCD) binds covalently to the conserved acidic residue in the c-subunit of Fo. One DCCD per ATP-ase is sufficient to block turn-over, suggesting a cooperative mechanism. The action of these inhibitors indicates that the proton permeability of the Fo is a part of its functional mechanism.
The proton leak can be plugged, and a functional ATP synthase can be reconstituted, by adding back the F1 portion to membranes containing the Fo portion.
The ATP synthase enzymes have been remarkably conserved through evolution. The bacterial enzymes are essentially the same in structure and function as those from mitochondria of animals, plants and fungi, and the chloroplasts of plants. The early ancestory of the enzyme is seen in the fact that the Archaea have an enzyme which is clearly closely related, but has significant differences from the Eubacterial branch. The H+-ATP-ase found in vacuoles of the eukaryote cell cytoplasm is similar to the archaeal enzyme, and is thought to reflect the origin from an archaeal ancestor.
In most systems, the ATP synthase sits in the membrane (the "coupling" membrane), and catalyses the synthesis of ATP from ADP and phosphate driven by a flux of protons across the membrane down the proton gradient generated by electron transfer. The flux goes from the protochemically positive (P) side (high proton electrochemical potential) to the protochemically negative (N) side. The reaction catalyzed by ATP synthase is fully reversible, so ATP hydrolysis generates a proton gradient by a reversal of this flux. In some bacteria, the main function is to operate in the ATP hydrolysis direction, using ATP generated by fermentative metabolism to provide a proton gradient to drive substrate accumulation, and maintain ionic balance.