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Proton-translocating ATPases are ubiquitous protein complexes that couple ATP catalysis with proton translocation via a rotary catalytic mechanism. The peripheral stalks are essential components that counteract torque generated from proton translocation during ATP synthesis or from ATP hydrolysis during proton pumping. Despite their essential role, the peripheral stalks are the least conserved component of the complexes, differing substantially between subtypes in composition and stoichiometry. We have determined the crystal structure of the peripheral stalk of the A-type ATPase/synthase from Thermus thermophilus consisting of subunits E and G. The structure contains a heterodimeric right-handed coiled coil, a protein fold never observed before. We have fitted this structure into the 23-Å resolution electron microscopy density of the intact A-ATPase complex, revealing the precise location of the peripheral stalk and new implications for the function and assembly of proton-translocating ATPases.

Rotary ATPases couple ATP hydrolysis/synthesis with proton translocation across biological membranes and so are central components of the biological energy conversion machinery. Their peripheral stalks are essential components that counteract torque generated by rotation of the central stalk during ATP synthesis or hydrolysis. Here we present a 2.25-Å resolution crystal structure of the peripheral stalk from Thermus thermophilus A-type ATPase/synthase. We identify bending and twisting motions inherent within the structure that accommodate and complement a radial wobbling of the ATPase headgroup as it progresses through its catalytic cycles, while still retaining azimuthal stiffness necessary to counteract rotation of the central stalk. The conformational freedom of the peripheral stalk is dictated by its unusual right-handed coiled-coil architecture, which is in principle conserved across all rotary ATPases. In context of the intact enzyme, the dynamics of the peripheral stalks provides a potential mechanism for cooperativity between distant parts of rotary ATPases.

Proton-translocating ATPases are central to biological energy conversion. Although eukaryotes contain specialized F-ATPases for ATP synthesis and V-ATPases for proton pumping, eubacteria and archaea typically contain only one enzyme for both tasks. Although many eubacteria contain ATPases of the F-type, some eubacteria and all known archaea contain ATPases of the A-type. A-ATPases are closely related to V-ATPases but simpler in design. Although the nucleotidebinding and transmembrane rotor subunits share sequence homology between A-, V-, and F-ATPases, the peripheral stalk is strikingly different in sequence, composition, and stoichiometry. We have analyzed the peripheral stalk of Thermus thermophilus A-ATPase by using phage display-derived single-domain antibody fragments in combination with electron microscopy and tandem mass spectrometry. Our data provide the first direct evidence for the existence of two peripheral stalks in the A-ATPase, each one composed of heterodimers of subunits E and G arranged symmetrically around the soluble A 1 domain. To our knowledge, this is the first description of phage display-derived antibody selection against a multi-subunit membrane protein used for purification and single particle analysis by electron microscopy. It is also the first instance of the derivation of subunit stoichiometry by tandem mass spectrometry to an intact membrane protein complex. Both approaches could be applicable to the structural analysis of other membrane protein complexes.F-, V-, and A-ATPases 2 are evolutionary related protein complexes (1) that couple ATP synthesis/hydrolysis with proton (or Na ϩ ) translocation across membranes (2-4). A-and V-ATPases are evolutionarily closer to each other than they are to F-ATPases (5). However, A-ATPases are functionally more similar to F-ATPases because both synthesize ATP using energy derived from proton translocation (5). V-ATPases work in reverse by actively pumping protons through membranes using ATP hydrolysis as the driving force (6).Although eukaryotes contain both types of ATPases, each one highly specialized in its physiological function, archaea and eubacteria typically contain only one. Both eubacterial F-ATPases and eubacterial and archaeal V-ATPases are simpler than their eukaryotic counterparts but are functionally more versatile in that they can operate in both directions. Archaeal and eubacterial V-ATPases are closely related and are often referred to as A-ATPases (4).F-, V-, and A-ATPases share an overall conservation of structure that includes a water-soluble F 1 /V 1 /A 1 domain and a membrane-bound F o /V o /A o domain (7-10). The Thermus thermophilus ATPase-active A 1 domain is composed of a head group that contains a heterotrimer of the nucleotide-binding proteins A and B and a central stalk composed of proteins C, D, and F (11). The proton-translocating A o domain contains a ring of L proteolipids and a single copy of protein I that is located adjacent to the ring. The L ring, in association with the central stalk components (CDF), for...

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