3.A.2 The H+- or Na+-translocating F-type, V-type and A-type ATPase (F-ATPase) Superfamily
F-type ATPases are found in eukaryotic mitochondria and chloroplasts as well as in bacteria. V-type ATPases are found in vacuoles of eukaryotes and in bacteria. A-type ATPases are found in archaea. All such systems are multisubunit complexes with at least 3 dissimilar subunits embedded as a complex in the membrane (F0, a:b:c = 1:2:~12) and (usually) at least 5 dissimilar subunits attached to F0 (F1, α:β:γ:δ:ε = 3:3:1:1:1 for F-type ATPases). The eukaryotic proteins are more complicated than the bacterial enzyme complexes. The a, b, δ and F1 hexamer (α3β3) comprise the stator. The rotor (which consists of the c, ε and γ subunits) is believed to rotate relative to the stator in response to either ATP hydrolysis by F1 or proton transport through F0. H+ transport and ATP synthesis may therefore be coupled mechanically. The F1 portion of the bovine mitochondrial F-type ATPase has been solved to 2.8 Å resolution. Cross-linking studies suggest that the H+ channel consists of a and c subunits where the external aqueous access channel is located to the inside of the a-subunit 4-helix bundle (Schwem and Fillingame, 2006). Minimal requirements for proton translocation by the ATP synthase include a positive charge in subunit a and a weak interface between subunit a and oligomeric subunit c (Ishmukhametov et al., 2007). These enzymes can pump H+ or Na+. A Na+ A-type ATPase from Pyrococcus furiosus has been described (Pisa et al., 2007b). ATP binding to the ε-subunit plays a regulatory role; ATP binding may stabilize the ATPase-active form by fixing the ε-subunit into the folded conformation (Kato et al., 2007). Mechanisms of coupling H+ movement to ATP synthesis, based on structural data for the a and c subunits, have been proposed (Allegretti et al. 2015). The asymmetric features of the a subunit make it the master regulator determining which of the two functions, ATP production or ATP dissipation, will be performed (Nesci et al. 2015). The structure of the a subunit (5ARA) reveals an unusual two transmembrane α-helices at a 70° angle to the plane of the membrane (Tsirigos et al. 2017). The 3.6 Å structure of the yeast Fo domain has been solved by cryoEM, revealing how the protons travel through the complex, how the complex dimerizes, and how the dimers bend the membrane to produce cristae (Guo et al. 2017). The crystal structure of the S. cerevisiae c-subunit ring with bound oligomycin revealed the inhibitor docked on the outer face of the proton-binding sites, deep in the transmembrane region (Zhou and Faraldo-Gómez 2018). A torque-coupled thermodynamic model of the F--ATPase has been proposed (Ai et al. 2017). Electron cryomicroscopy structures of mitochondrial, chloroplast, and bacterial ATP synthases have revealed the architecture of the FO region, helping to explain the mechanisms of proton translocation, dimerization of the enzyme in mitochondria, and cristae formation. These structures also show that ATP synthases exist in different conformational states, illustrating the flexibility and dynamics of these complexex (Guo and Rubinstein 2018).
All eukaryotic F-type ATPases pump 3-4 H+ out of mitochondria, or into thylakoids of chloroplasts, per ATP hydrolyzed. ATP-driven stepwise rotation of FoF1-ATP synthase has been defined (Ueno et al. 2005). Bacterial F-type ATPases pump 3-4 H+ and/or Na+ (depending on the system) out of the cell per ATP hydrolyzed. These enzymes also operate in the opposite direction, synthesizing ATP when protons or Na+ flow through the 'ATP synthase' down the proton electrochemical gradient (the 'proton motive force' or pmf) (Ferguson et al., 2006). V-type ATPases may pump 2-3 H+ per ATP hydrolyzed, and these enzymes cannot catalyze pmf-driven ATP synthesis. It has been proposed that this difference between F-type and V-type ATPases is due to a 'proton slip' that results from an altered structure in the membrane sector of V-type ATPases (Perzov et al., 2001). This probably results from duplication (intragenic and/or intergenic) of the proteolipid (c) subunit. Several intact F-type ATPase complexes have been purified from different fungal species and analyzed for their properties and subunit comopositions after solubilization with various detergents (Liu et al. 2015). Purified mitochondrial F-ATP synthase forms a Ca2+-dependent high-conductance channel matching the mitochondrial permeability transition pore (Urbani et al. 2019).
The structure of the membrane integral rotor ring of the proton translocating F(1)F(0)-ATPase synthase from spinach chloroplasts was determined to 3.8 A resolution by X-ray crystallography (Vollmar et al., 2009). The rotor ring consists of 14 identical protomers which are symmetrically arranged around a central pore, but rings having anywhere from 8 protomers to 15 protomers have been reported (Watt et al., 2010). Comparisons to the c(11)-rotor ring of the sodium translocating ATPase from Ilyobacter tartaricus show that the conserved carboxylates involved in proton or sodium transport, respectively, are 10.6-10.8 A apart in both c-ring rotors. This finding suggests that both ATPases have the same gear distance despite their different stoichiometries. The putative proton binding site at the conserved carboxylate E61 in the chloroplast ATP synthase differs from the sodium binding site in Ilyobacter. Residues adjacent to the conserved carboxylate show increased hydrophobicity and reduced hydrogen bonding. The crystal structure reflects the protonated form of the chloroplast c-ring rotor. Vollmar et al., 2009 proposed that upon deprotonation, the conformation of E61 is changed to another rotamer and becomes fully exposed to the periphery of the ring. Reprotonation of E61 by a conserved arginine in the adjacent a subunit returns the carboxylate to its initial conformation. The structure of the c-ring has been examined in different lipid bilayers (Kang et al. 2018). F-type ATPases can be inhibited by ADP (Lapashina and Feniouk 2018). Amino acids in the FO sector that influence H+ translocation have been identified (Trombetti et al. 2019).
Phylogenetic clustering of the integral membrane constituents of F-type ATPases generally corresponds to the phylogenies of the organisms of origin, and consequently the systems in different organisms are probably orthologues. The a subunit of F0 (one copy per complex) spans the membrane five or six times. The b subunits (2 copies per complex; heterodimeric in plant chloroplasts and blue green bacteria) span the membrane once; and the c subunits (called DCCD-binding lipoproteins; reportedly 10, 11, 12, or 14 copies per complex depending on the system) span the membrane two times. Some F-type ATPases such as the Na+-translocating ATPase of Acetobacterium woodii probably contains 3 dissimilar but homologous c-subunit proteolipids of 8 and 18 kDa. The V-type ATPase of S. cerevisiae also has 3 dissimilar c-subunits as mentioned in the next paragraph. While c-subunits in the E. coli F-ATPase have 2 TMSs (one acive site asp per subunit and 12 copies per complex), V-type ATPases have 4 TMSs (one active site glu per subunit and 6 copies per complex), and an archaeal A-ATPase has 6 TMSs (2 active site glus per subunit and 4 subunits per complex).
The α, β and c-subunits of F-type ATPases are homologues to the B, A and c- (or K-) subunits of V-type and A-type ATPases, respectively. Other subunits in these protein complexes are probably homologous to each other, but this fact cannot always be demonstrated by statistical analyses of the sequences. Thus, for the A-type ATPase of Methanosarcina mazei, the V-type ATPase of yeast, and the F-type ATPase of E. coli, respectively, the following subunit equivalences have been suggested: A = Vma1 (A) = β; B = Vma2 (B) = α; C = Vma6 (d) = no E. coli F-type ATPase equivalent; Vma8 (D) = γ; Vma4 (E) = δ; F = Vma7 (F) = ε; I = Vphl/stvl = a+b ?, and K = Vma3 (c) = c. Additionally, the yeast V-type ATPase has 3 dissimilar c-subunits: Vma3(c), Vmal1(c') and Vma6(c''), and three subunits, Vma13(H), Vma5(c) and Vma10(G) which are not found in either the A- or F-type ATPases. All of the yeast vacuolar ATPase subunits have an equivalent subunit in the V-type ATPases of clathrin-coated vesicles of higher eukaryotes.
Eukaryotic V-type ATPases acidify Golgi-derived vesicles, clathrin-coated vesicles, synaptic vesicles, liposomes, and plant vacuoles and function in protein trafficking, receptor-mediated endocytosis, neurotransmitter release, pH regulation, waste management, pro-hormone processing, protein degradation, etc (Kane, 2006). They also function in the entry of various pathogenic agents, including many envelope viruses, like influenza virus, and toxins, like anthrax toxin. Plasma membrane V-ATPases function in renal pH homeostasis, bone resorption and sperm maturation, and various disease processes, including renal tubular acidosis, osteopetrosis, and tumor metastasis (Toei et al., 2010). There are 13 subunits, 8 (A-H) in V1 and 5 (a, c, c', c'', d and e). The c-subunits are arranged in a ring with the a-subunit on the outside of the ring. The proton channel may be at the a/c interface, and c rotates relative to a when ATP is hydrolyzed and H+ is translocated. Rotation of V-type ATPases has been demonstrated (Imamura et al., 2003). Two important mechanisms of regulating V-ATPase activity in vivo are reversible dissociation of the V1 and V0 domains and changes in coupling efficiency of proton transport and ATP hydrolysis (Cipriano et al. 2008). V-type ATPase proteolipids can form symmetrical 6-membered rings as is true for gap junction sheets from Nephrops norvegicus which are formed by a protein identical to the 4 TMS V-ATPase c-subunit. A 14th subunit, Ac45, associated with V0, is found in some mammalian tissues. The crystal structure of the central axis DF complex of a prokaryotic V-ATPase has been solved (Saijo et al., 2011).
By altering the pH of intracellular compartments, V-ATPases dictate enzyme activities, govern the dissociation of ligands from receptors and promote the coupled transport of substrates across membranes. In tissues where V-ATPases are expressed at the plasma membrane, they can serve to acidify the extracellular microenvironment. Additional roles that seem independent of H+ translocation include fusogenicity, cytoskeletal tethering and metabolic sensing (Maxson and Grinstein 2014). CryoEM studies have revealed conformational heterogeneity and characteristic TMSs that are highly tilted with respect to the membrane (Mazhab-Jafari and Rubinstein 2016). An oscillating electric (AC) field has been used to measure the biochemical activity of a rotary enzyme such as a vacuolar proton-ATPase (V-ATPase), specificallly to directly measure its mean rate of rotation in its native membrane environment (Ferencz et al. 2017).
V-ATPase is a ~1 MDa membrane protein complex that functions in the acidification of endosomal/lysosomal compartments and hence in transport, recycling and degradative pathways. The complex, assembled from up to 30 individual polypeptides, operates as a molecular motor with rotary mechanics. Structural inferences about the eukaryotic V-ATPase and its subunits have been made by comparison to the structures of bacterial homologues. However, cryo-EM has revealed more about the catalytic mechanism of this proton pump and how its activity might be regulated in response to cellular signals (Harrison and Muench 2018).
In mammalian cells, most of the V-ATPase subunits exist in multiple isoforms which are often expressed in a tissue specific manner. Isoforms of one of the V(0) subunits (subunit a) have been shown to possess information that targets the V-ATPase to distinct cellular destinations. Mutations in isoforms of subunit a lead to the human diseases osteopetrosis and renal tubular acidosis. The Vesicular proton pump (V-ATPase) in nerve terminals following exocytosis continues to pump, promoting neurotransmitter uptake via endocytosis (Tabares and Betz, 2010). A number of mechanisms are employed to regulate V-ATPase activity in vivo, including reversible dissociation of the V(1) and V(0) domains, control of the tightness of coupling of proton transport and ATP hydrolysis, and selective targeting of V-ATPases to distinct cellular membranes. Isoforms of subunit a are involved in regulation both via the control of coupling and via selective targeting (Toei et al., 2010).
The V-ATPase ring contains three different subunits, c, c' and c'' and is therefore probably asymmetric if two or all three are present. In the yeast vacuolar ATPase, C (VMA3p) and C' (VMA11p) are 4 TMS proteins with N- and C-termini in the vacuolar lumen, but C'' (VMA16p) is a 5 TMS protein with N-terminus in the cytosol and the C-terminus in the lumen (Flannery et al., 2004). Althought TMHMM predicts 7TMSs for the a subunit (P32563) of the yeast (S. cerevisiae) V-type ATPase, Wang et al (2008) provide evidence for an eight transmembrane helix model in which the C-terminus is located on the cytoplasmic side of the membrane. By angular reconstitution from electron microscopic images, a 21 Å resolution structure shows an asymmetric protein ring with two small openings on the lumenal side and one large opening on the cytoplasmic side. The central hole on the lumenal side is covered by a globular protein while the cytoplasmic opening is covered by two elongated proteins (Wilkens and Forgac, 2001). Evolution of the hexameric transmembrane ring of the eukaryotic V-ATPase proton pump has been investigated (Finnigan et al., 2012).
In the reversible coupled rotatory mechanism for ATP-hydrolysis driven H+ transport, the coupling scheme is now basically complete. During rotation of single molecules of F1, phosphate release drives the last 40° of the 120° step, and the 40° rotation accompanies reduction of the affinity for phosphate. Moreover, the affinity for ADP decreases with rotation, and thus, ADP release contributes part of energy for rotation (Adachi et al., 2007; Senior, 2007). Surprisingly, Uchihashi et al. (2011), using high speed atomic force microscopy, have shown that the F1 ATPase exhibits rotary catalysis in the absence of the rotor. Post-translational modifications modulate both the F0 and F1 proteins, affecting the ATPase activity in response to different stimuli (Nesci et al. 2017).
The rotary proton- and sodium-translocating ATPases are reversible molecular machines present in all cellular life forms that couple ion movement across membranes with ATP hydrolysis or synthesis. Sequence and structural comparisons of F- and V-type ATPases have revealed homology between their catalytic and membrane subunits, but not between the subunits of the central stalk that connects the catalytic and membrane components. It has been proposed that these ATPases originated from membrane protein translocases which evolved from RNA translocases (Mulkidjanian et al., 2007). The Na+-pumping ATP synthase of Acetobacterium woodii has an unusual feature: its membrane-embedded rotor is a hybrid made of F and V-like subunits in a stoichiometry of 9:1, apparently not variable with the growth conditions (Schmidt et al., 2009).
Bacterial operons for F(1)F(0)-ATP synthase typically include an uncI gene encodes a small hydrophobic protein. When Suzuki et al. (2007) expressed a hybrid F(1)F(0) (F(1) from thermophilic Bacillus PS3 and Na+-translocating F(0) from Propionigenium modestum) in E. coli cells, they found that uncI derived from P. modestum was indispensable to produce active enzyme; without uncI, c-subunits in F(1)F(0) existed as monomers but not as a functional c(11)-ring. A plasmid containing only uncI and the c-subunit gene produced c(11)-ring, but a plasmid containing only the c-subunit gene did not. Direct interaction of the UncI protein with c-subunits was demonstrated. Na+ induced dissociation of His-tagged UncI protein from the c(11)-ring but not from c-monomers. Thus, UncI is a chaperone-like protein that assists the c(11)-ring assembly from the c-monomers in the membrane (Suzuki et al., 2007). Ozaki et al., (2008) have confirmed these observations. The halotolerant cyanobacterium, Aphanothece halophytica, contains an Na+-dependent F1F0-ATP synthase with a potential role in salt-stress tolerance (Soontharapirakkul et al., 2011).
The prokaryotic V-ATPase of Enterococcus hirae, closely related to the eukaryotic enzymes, provides a unique opportunity to study ion translocation by V-ATPases because it transports Na+ ions, which are easier to detect by x-ray crystallography and radioisotope experiments (Murata et al., 2008). The purified rotor ring (K-ring) of the E. hirae V-ATPase binds one Na+ ion per K-monomer with high affinity, which is competitively inhibited by Li+ or H+. The K-ring structure was determined at 2.8 A in the presence of Li+. Association and dissociation rates of the Na+ to and from the purified K-ring were extremely slow compared with the Na+ translocation rate estimated from the enzymatic activity, suggesting that interaction with the stator subunit (I-subunit) is essential for Na+ binding to and release from the K-ring.
Subunit a of the vacuolar H+-ATPases is an integral membrane 100kDa subunit, thought to contribute to and leave buried carboxyl groups on the proteolipid subunits (c, c' and c'') during proton translocation. Subunit a contains a large N-terminal cytoplasmic domain followed by a C-terminal domain containing eight transmembrane (TM) helices. TM7 contains a buried arginine residue (Arg-735) that is essential for proton transport and is located on a helical face that interacts with the proteolipid ring (Toei et al., 2011). Residues important for proton transport are located on the cytoplasmic half of TM7 and TM8 and the luminal half of TM3, TM4 and TM7. The cytoplasmic hemi-channel is located at the interface of TM7 and TM8 of subunit a and the proteolipid ring, whereas the luminal hemi-channel is located within subunit a at the interface of TM3, TM4 and TM7.
Rotary ATPases/synthases from Thermus thermophilus and Enterococcus hirae are maintained intact with membrane and soluble subunit interactions preserved in vacuum. Mass spectra reveal subunit stoichiometries and the identity of tightly bound lipids within the membrane rotors. Moreover, subcomplexes formed in solution and gas phases reveal the regulatory effects of nucleotide binding on both ATP hydrolysis and proton translocation. Consequently, specific lipid and nucleotide binding can be linked with distinct regulatory roles (Zhou et al., 2011).
Rotations of F1-ATPase occurs reversibly in discrete 120° steps by precisely controlling both the external torque and the chemical potential of ATP hydrolysis. Toyabe et al. (2011) found that the maximal work performed by F1-ATPase per 120° step is nearly equal to the thermodynamic maximal work that can be extracted from a single ATP hydrolysis event under a broad range of conditions. Their results support a nearly 100% free-energy transduction efficiency and a tight mechanochemical coupling.
The ability of c-rings to rotate within the F(o) complex derives from the interplay between the ion-binding sites and their nonhomogenous microenvironment (Pogoryelov et al., 2010). Pogoryelov et al. (2010) demonstrated how the thermodynamic stability of the so-called proton-locked state is maximized by the lipid membrane. By contrast, a hydrophilic environment at the a-subunit-c-ring interface appears to unlock the binding-site conformation and promotes proton exchange with the surrounding solution. Rotation thus occurs as c-subunits stochastically alternate between these environments, directionally biased by the electrochemical transmembrane gradient. Intrinsic features of the annular arrangement of c subunits, the c-ring, provides the core of the membrane-embedded FO domain. The c-ring constitution is linked to the number of ions, H+ or Na+, channeled across the membrane during the dissipation of the transmembrane electrochemical gradient, which in turn determines the species-specific bioenergetic cost of ATP, the 'molecular currency unit' of energy transfer (Nesci et al. 2016).
Allegretti et al. 2015 reported the structure of a native, active mitochondrial ATP synthase dimer, determined by single- particle electron cryomicroscopy at 6.2 Å resolution. The structure showed four long, horizontal membrane-intrinsic α-helices in the a-subunit, arranged in two hairpins at an angle of approximately 70 degrees relative to the c-ring helices. It had been proposed that a strictly conserved membrane-embedded arginine in the a-subunit couples proton translocation to c-ring rotation. A fit of the conserved carboxy-terminal a-subunit sequence places the conserved arginine next to a proton-binding c-subunit glutamate. The map shows a slanting solvent-accessible channel that extends from the mitochondrial matrix to the conserved arginine. Another hydrophilic cavity on the lumenal membrane surface defines a direct route for the protons to an essential histidine-glutamate pair. The results explain how ATP production is coupled to proton translocation (Allegretti et al. 2015).
The molecular structure of the transmembrane domain of ATP synthases is responsible for inner mitochondrial membrane bending. According to a hypothesized mechanism, ATP synthase dissociation from dimers to monomers, triggered by Ca2+ binding to F1, allows mitochondrial permeability transition pore formation at the interface between the detached monomers (Nesci 2018).
Bedaquiline (BDQ, trade name Sirturo) for the treatment of multidrug-resistant tuberculosis disease, targets the membrane-bound F1Fo-ATP synthase and is a respiratory 'uncoupler', disrupting transmembrane electrochemical gradients, in addition to binding to enzyme targets. Hards and Cook 2018 summarized the role of bioenergetic systems in mycobacterial persistence and discuss the multi-targeting nature of uncouplers and the place these molecules may have in future drug development.
An arginine residue (Arg-735) in transmembrane helix 7 (TM7) of subunit a of the yeast ATPase is known to be essential for proton translocation. Arginine residues are usually assumed to 'snorkel' toward the protein surface when exposed to a hydrophobic environment. However, Hohlweg et al. 2018 obtained evidence for the formation of a transient, membrane-embedded cation-π interaction in TM7 between Arg-735 and two highly conserved nearby aromatic residues, Tyr-733 and Trp-737. They proposed a mechanism by which the transient, membrane-embedded cation-π complex provides the necessary energy to keep the charged side chain of Arg-735 within the hydrophobic membrane. Such cation-π interactions may define a general mechanism to retain charged amino acids in a hydrophobic membrane environment (Hohlweg et al. 2018).
The generalized transport reaction for F-type, V-type and A-type ATPases is:
nH+ (in) [or nNa+ (in)] + ATP nH+ (out) [or nNa+ (out)] + ADP + Pi
H+-translocating F-type ATPase. The loop-regions in subunits a and c that are implicated in H+ transport likely interact in a single structural domain which then functions in gating H+ release to the cytoplasm (Steed et al. 2014). Three different states that relate to rotation of the enzyme have been observed, with the central stalk's epsilon subunit in an extended autoinhibitory conformation in all three states (Sobti et al. 2016). The Fo motor consists of seven transmembrane helices and a decameric c-ring, and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by ~30 degrees to the membrane, a feature corresponding to rotary ATPases. This rotary ATPase subtype, the peripheral stalk, is resolved over the entire length of the complex, revealing the F1 attachment points and a coiled-coil that bifurcates toward the membrane with its helices separating to embrace subunit a from two sides (Sobti et al. 2016).
Bacteria; eukaryotic mitochondria and chloroplast
F-type ATPase of E. coli
H+-transporting F-type ATPase (Soontharapirakkul et al. 2011). This halotolerant cyanobacterium has two F-type ATPases, one pumping H+, and one pumping Na+ (see TC# 3.A.2.1.9).
Na+-ATPase of Aphanotheca halophytica
α, 505 aas
β, 484 aas
γ, 317 aas
δ, 187 aas
ε, 138 aas
a, 257 aas
b, 256 aas
b', 182 aas
c, 81 aas
F-type ATP synthase of 8 subunits common to other ATPases, and 9 subunits unique to the Chlorophyta. Near neighbor interactions of the membrane subunits have been measured (Sánchez-Vásquez et al. 2017). The spinich enzyme has been solved at 3.4 Å resolution by cryoEM (Hahn et al. 2018). The protein has 26 protein subunits, 17 of them membrane embedded. Its c-ring has 14 c subunits. Hahn et al. 2018 observed 3 chloroplast F1F0 conformations with the central rotor stalled in different positions, and ring rotation seemed to be divided into 3 unequal stteps. The stoichiometrically mismatched c-ring of F0s (composed of 8 to 17 c-subunits) and the 3-fold symmetric F1 head are flexibly coupled (Murphy et al. 2019). Based on cryo EM 2.7 Å resolution structures, 13 rotary states suggest a mechanism of the rotational movement, and the functions of novel subunits are proposed (Murphy et al. 2019).
F-type ATP synthase of Polytomella sp. Pringsheim 198.80 (Subunits b and ε are not available, and several of the Asa subunits are partial.
subunit α, 562 aas (A0ZW40)
subunit β, 574 aas (A0ZW41)
subunit γ, 317 aas (Q4LDE7)
subunit δ, 199 aas (D7P7X6)
subunit ε, not available
subunit a (OSCP)229 aas, 6 TMSs
subunit b (not available)
subunit c, 127 aas, 2 TMSs
subunit ASA1, 918 aas, 0 TMSs (Q85JD5)
subunit ASA2, 383 aas, 0 TMSs (D7P6B9)
subunit ASA3, 167 aas, 0 TMSs (D7P8N0)
subunit ASA4, 294 aas, 0 TMSs (D7NIZ2)
subunit ASA5, 123 aas and 0 TMSs (CBM40331.1)
subunit ASA6, 151 aas and 1 TMS (D7P897)
subunit ASA7, 190 aas, 0 TMSs (D8V7I2)
subunit ASA8, 89 aas, 1 TMS (D8V7I7)
F-type ATPase lacking a δ-subunit, but having another subunit, AtpR of 104 aas and 3 TMSs that may replace the δ-subunit. Has a c-subunit that shows the expected residues that comprise a Na+ binding site, so it may be a Na+ exporting ATPase. It is in a family of similar ATPases that all lack δ-subunits and have been called N-ATPases (Na+-transporting) (Dibrova et al. 2010). They appear to be subject to horizontal transfer and represent a second type of F-type ATPase, the other transporting protons. They are found in a variety of bacteria and archaea (Dibrova et al. 2010). The AtpQ protein may be a Mg2+ channel.
N-type ATPase of Methanosarcina barkeri
AtpD, β-subunit, 474 aas
AtpC, subunit, 139 aas
AtpR, extra subunit; possibly replacing the δ-subunit; 104 aas and 3 TMSs
AtpQ, the Mg2+ channel protein belonging to family 1.A.77.2 with 112 aas and 2 TMSs
AtpB, subunit a, 229 aas
AtpE, subunit c, 91 aas
AtpF, subunit b, 413 aas
AtpA. subunit α, 571 aas
AtpG, subunit γ, 301 aas
F-type ATPase/ATP synthase of T. brucei. The F1 domain has been studied and examined in 3-dimentions at low resolution, and in addition to the 5 usual subunits, it has an extra one, called p18 of 188 aas (UniProt acc # P0DPG4). p18 is present in three copies per complex. Suppression of expression of p18 affected in vitro growth of both the insect and infectious mammalian forms of T. brucei. It also reduced the levels of monomeric and multimeric F-ATPase complexes and diminished the in vivo hydrolytic activity of the enzyme (Gahura et al. 2018). The p18 subunit, identified only in the euglenozoa, associates with the external surface of each of the three α-subunits. Subunit p18 is a pentatricopeptide repeat (PPR) protein with three PPRs and appears to have no function in the catalytic mechanism of the enzyme (Montgomery et al. 2018). Inhibitors include furamidine (DB75), Pafuramidine (DB289), DB820 and DB829 (Meier et al. 2018).
F1-part of the F-type ATP synthase of Trypanosoma brucei
α, 584 aas, Q9GS23
β, 519 aas, Q9GPE9
γ, 305 aas, B0Z0F6
δ, 182 aas, P0DPG2
ε, 75 aas, P0DPG3
p18, 188 aas, P0PDPG4
Na+-translocating F-type ATPase/ATP synthase of 8 subunits. The Fo-a subunit plays a role in Na+ transport. It forms half channels that allow Na+ to enter and leave the buried carboxyl group on the Fo-c subunits. The essential Arg residue, R226, which faces the carboxyl group of Fo-c subunits in the middle of transmembrane helix 5 of the Fo-a subunit, separates the cytoplasmic side and periplasmic half-channels (Mitome et al. 2017). Residues that contribute to the integrity of the Na+ half channels have been identified; both half channels are present in the Fo-a subunit (Mitome et al. 2017).
F-type ATPase of Propionigenium modestum
H+-translocating F-type ATPase. Evidence of the proximity of ATP synthase subunit 6 is in proximity to the membrane in the supramolecular form (Velours et al., 2011). The structure of the intact monomeric ATP synthase from the fungus, Pichia angusta, has been solved by electron cryo-microscopy (Vinothkumar et al. 2016). The Mg2+ and Ca2+-dependent enzymes are both active, but exhibit quite different behaviors (Nesci et al. 2017). Dimerization is necessary to create the inner membrane folds (cristae) characteristic of mitochondria. Using cryo-electron microscopy, Guo et al. 2017 determined the structure of the dimeric FO complex from Saccharomyces cerevisiae at a resolution of 3.6 angstroms. The structure clarifies how the protons travel through the complex, how the complex dimerizes, and how the dimers bend the membrane to produce cristae. The crystal structure of the c-subunit ring with bound oligomycin revealed the inhibitor docked on the outer face of the proton-binding sites, deep in the transmembrane region (Zhou and Faraldo-Gómez 2018). A high resolution (3.7 Å) structure of the entire monomeric ATPase has been solved by cryo EM, suggesting how it is inhibited by oligomycin (Srivastava et al. 2018). Absence of the e and g subunits decreases conductance of the F-ATP synthase channel about tenfold. Ablation of the first TMS of subunit b, which creates a distinct lateral domain with e and g, further affected channel activity. Thus, F-ATP synthase e, g and b subunits create a domain within the membrane that is critical for the generation of the high-conductance channel that is a prime candidate for formation of the permeability transition pore (PTP). Subunits e and g are only present in eukaryotes and may have evolved to confer this novel function to F-ATP synthases (Carraro et al. 2018).
F-type ATPase of Saccharomyces cerevisiae
Subunits ATP6; ATP8; ATP9; ATP1; ATP3; ATP16; ATP5; ATP2; ATP7; ATP14; ATP4; ATP15
The F-type ATPase of the ciliate, Tetrahymena thermophila (strain SB210). The eight established or putative ATPase subunits are provided. These are distantly related to subunits of other studied F-type ATPases (Balabaskaran Nina et al., 2010).Other associated proteins/subunits are presented by Balabaskaran Nina et al. (2010).
F-type ATPase of Tetrahymena thermophila strain SB210.
(1) F0 subunit 9 (subunit c) (76aas; 2 TMSs) (Q951A5)
(2) F1 %u03B4-subunit (OSCP) (219aas; 0 TMSs) (I7MMI7)
(3) F1 γ-subunit (299aas; 0 TMSs) (Q22Z05)
(4) F1 α-subunit (546aas; 0 TMSs) (Q24HY8)
(5) F1 β-subunit (497aas; 0 TMSs) (I7LZV1)
(6) hypothetical protein/putative F1 %u03B4 subunit (158aas; 0 TMSs) (Q22ZH1)
(7) hypothetical protein/putative F0 d subunit (234aas; 0 TMSs) (Q239R1)
(8) Ymf66/putative ATP synthase subunit a-like protein (446aas; 8 TMSs) (Q951C1)
The Na+-F1F0 ATP synthase. Has a hybrid rotor with 9 copies of an F0-like c-subunit with 1 ion binding site/2TMSs and 1 copy of a V0-like C1-subunit (with 1 ion binding site/4TMSs). The AtpI Mg2+ channel protein (TC# 1.A.77.10.4) is required for assembly of the hybrid rotor (Brandt et al. 2013).
F1F0-ATP synthase of Acetobacterium woodii
subunit size gene acc#
c2 82 atpE2 (Q59166)
c1 182 atpE1 (Q9RMB5)
α 502 atpA (P50000)
a 220 atpB (Q9RMB6)
δ 180 atpH (Q9RMB3)
b 184 atpF (Q9RMB4)
ε 133 atpC (P50009)
β 466 atpD (P50002)
γ 302 atpG (P50005)
F-type ATPase, AtpA-H
F-type ATPase of Parachlamydia acanthamoeba
AtpA, alpha, 504 aas
AtpB, a, 252 aas
AtpC, epsilon, 83 aas
AtpD, beta, 469 aas
AtpE, c, 77 aas
AtpF, b, 161 aas
AtpG, gamma, 286 aas
AtpH, delta, 183 aas
F-type ATPase. The enzyme can synthesize but not hydrolyze ATP due to the presence of the zeta inhibitor. The crystal structure is known (Morales-Rios et al. 2015). The complex that was crystallized contains the nine core proteins of the complete F-ATPase complex plus the zeta inhibitor protein. The formation of crystals depended upon the presence of bound bacterial cardiolipin and phospholipid molecules; when they were removed, the complex failed to crystallize.
F-type ATPase of Paracoccus denitrificans
Sodium (Na+)-pumping F-type ATPase. ATPase activity is stimulated by Na+ (Wiangnon et al. 2007), and Na+ transport in liposomes has been demostrated (Soontharapirakkul and Incharoensakdi 2010). The enzyme appears to play a role in salt tolerance (Soontharapirakkul et al. 2011). This halotolerant cyanobacterium has both a Na+- and a H+-pumping ATPase (see TC# 3.A.2.1.10). The sequence of the δ-subunit was not available at the time of entry.
Na+-ATPase of Aphanotheca halophytica
α, 514 aas
β, 470 aas
γ, 303 aas
δ, sequence not available
ε, 128 aas
a, 232 aas
b, 256 aas
c, 96 aa
H+-translocating V-type ATPase. The 3-D structure is known (Lau and Rubinstein, 2012). More recently, Zhou and Sazanov 2019 solved cryo-EM structures of the intact Thermus thermophilus V/A-ATPase in three rotational states with two substates. These structures indicate substantial flexibility between V1 and Vo in a working enzyme, which results from mechanical competition between central shaft rotation and resistance from the peripheral stalks.
V-type ATPase of Thermus thermophilus
Na+-translocating V-type ATPase. The V-ATPase of E. hirae (EhV-ATPase) is composed of a soluble catalytic domain (V1; NtpA3-B3-D-G) and an integral membrane domain (V0; NtpI-K10) connected by a central and two peripheral stalks (NtpC, NtpD-G and NtpE-F) (see schematic figure 1 on pg. 60 of Muhammed et al., 2012). The membrane rotor ring of the Na+-ATPase consists of 10 NtpK subunits, which are homologs of the 16-KDa and 8-KDa proteolipids found in other V-ATPases and F-ATPases. Each NtpK subunit has four transmembrane alpha helices, with a sodium ion bound between helices 2 and 4 at a site buried deeply in the membrane that includes the essential residue glutamate-139 (Murata et al. 2005). This site is probably connected to the membrane surface by two half-channels in subunit NtpI, against which the ring rotates. Symmetry mismatch between the rotor and catalytic domains appears to be an intrinsic feature of both V- and F-ATPases (Murata et al. 2005). The EhV-ATPase is a Na+ pump in. Tsunoda et al. 2018 presented the entire structure of detergent-solubilized EhV-ATPase by single-particle cryo-EM using Zernike phase plates. The cryo-EM map showed one of three catalytic conformations. To further stabilize the originally heterogeneous structure caused by ATP hydrolysis, a peptide epitope tag system interfered with rotation of the central rotor by binding the Fab. As a result, the map unexpectedly showed another catalytic conformation of EhV-ATPase. These two conformations with and without Fab conversely coincided with those of the minor state 2 and the major state 1 of Thermus thermophilus V/A-ATPase, respectively. The most prominent feature in EhV-ATPase was the off-axis rotor, where the cytoplasmic V1 domain was connected to the Vo domain through the off-axis central rotor. Compared to the structure of ATP synthases, the larger size of the interface between the transmembrane a-subunit and c-ring of EhV-ATPase would be more advantageous for active ion pumping (Tsunoda et al. 2018).
V-type ATPase of Enterococcus hirae
NtpC (NtpP) (P43456)
NtpE (NtpO) (P43436)
NtpF (NtpL) (P43437)
NtpG (NtpQ) (P43455)
NtpI (NtpM) (P43439)
NtpK (NtpN) (P43457)
H+-translocating V-type ATPase. The d-subunit couples ATP hydrolysis to H+ transport (Owegi et al., 2006). The a subunit (Vph1p) most likely has an 8 TMS topology (Kartner et al. 2013; Knight and Behm 2012). Structures for three
rotational states show ten proteolipid subunits in the c-ring, setting the ATP:H+ ratio for proton
pumping. Long tilted TMSs in
the a-subunit interact with the c-ring. V-ATPase's membrane sector, Vo, has been implicated in functions including
membrane fusion and neurotransmitter release. Couoh-Cardel et al. 2016 reported that the purified V-ATPase c subunit ring (c-ring) forms dimers mediated by the c subunits'
cytoplasmic loops. Electrophysiological measurements of the c-ring reconstituted into a planar lipid
bilayer revealed a large unitary conductance of ~8.3 nS. A role of the
c-ring in membrane fusion and neuronal communication was suggested (Couoh-Cardel et al. 2016).
The three different maps reveal the conformational changes that occur to couple rotation in the symmetry-mismatched soluble catalytic region to the membrane-bound proton-translocating region. Almost all of the subunits undergo conformational changes during the transitions between these three rotational states (Zhao et al. 2015). The structures of these states provide direct evidence that deformation during rotation enables the smooth transmission of power through rotary ATPases. Increases in glucose stimulate V-ATPase assembly and activity while glucose deprivation triggers rapid V-ATPase disassembly and inactivation in yeast. However, the opposite phenomenon is observed in mammalian cells, specifically that V-ATPase assembly and activation increases when glucose is lost (Parra and Hayek 2018).
The 3.5 Å resolution cryoEM structure of the lipid nanodisc-reconstituted Vo proton channel, captured in a physiologically relevant autoinhibited state, revealing the residues that constitute the proton pathway at the interface of the proteolipid ring and subunit a has been solved (Roh et al. 2018). The chemical basis of transmembrane proton transport was proposed. Roh et al. 2018 discovered that the C terminus of the assembly factor Voa1 (TC# 9.B.206.2.1)) is an integral component of the mature Vo. Voa1's C-terminal transmembrane alpha helix is bound inside the proteolipid ring, where it contributes to the stability of the complex. The structure rationalizes possible mechanisms by which mutations in human Vo can result in disease phenotypes.
An arginine residue (Arg-735) in transmembrane helix 7 (TMS7) of subunit a of the yeast ATPase is known to be essential for proton translocation. Arginine residues are usually assumed to 'snorkel' toward the protein surface when exposed to a hydrophobic environment. However, Hohlweg et al. 2018 obtained evidence for the formation of a transient, membrane-embedded cation-π interaction in TM7 between Arg-735 and two highly conserved nearby aromatic residues, Tyr-733 and Trp-737. They proposed a mechanism by which the transient, membrane-embedded cation-π complex provides the necessary energy to keep the charged side chain of Arg-735 within the hydrophobic membrane. Such cation-π interactions may define a general mechanism to retain charged amino acids in a hydrophobic membrane environment (Hohlweg et al. 2018).
V-type ATPase of Saccharomyces cerevisiae
CUP5 (c1; VMA3)
VPH1 (a1; vacuole)
STV1 (a; Golgi) (P37296)
VMA9 (e) (Q3E7B6)
VMA16 (C'') (P23968)
The ubiquitous 14 subunit vacuolar H+-ATPase, V1/V0, has been implicated in various human diseases including osteopetrosis, renal tubule acidosis, and cancer (Hinton et al., 2009). The transmembrane enzyme, Ribonuclease kappa, RNASEK (137 aas; 2 TMSs; UniProt acc# Q6P5S7), closely associates with the V-ATPase and is required for its function; its loss prevents the early events of endocytosis and the replication of multiple pathogenic viruses (Perreira et al. 2015).
14 subunits of the V-type ATPase of Homo sapiens
H -translocating V-type ATPase (Dettmer et al., 2006). The mung bean (Phaseolus aureus) subunits a and c (c'' and c") alone catalyze passive channel-mediated protein flux, but a c d did not (Ouyang et al., 2008). A 4 TMS c-subunit of Tamarix hispida (onion), almost identical to the c-subunit of the A. thaliana homologue, plays a stress tolerance role in response to salt, drought, UV, oxidation, heat, cold, and heavy metals (Gao et al. 2011). The VHA-H subunit is up-regluated upon high salt stress conditions (Yang et al. 2018).
V-type ATPase of Arabidopsis thaliana
H+-translocating V-type ATPase (Knight and Behm 2012). The c-subunit, ATP6V0C is upregulated by the drug against L. donovani, naloxonazine (De Muylder et al. 2016).
V-type ATPase of Mus musculus
H+-translocating V-type ATPase (Knight and Behm 2012).
V-type ATPase of Caenorhabditis elegans
V-type ATPase with 13 subunits
V-type ATPase of Paramecium tetraurelia
VatA1_1, 832 aas (Q6BFK1)
VatA2_1, 906 aas (Q3SDD1)
VatA3_1, 800 aas (Q3SDC9)
VatA4_1, 772 aas (Q3SDC7)
VatA5_1, 850 aas (Q3SDC6)
VatA6_1, 831 aas (Q3SDC5)
VatA7_1, 768 aas (Q3SDC3)
VatA8_1, 793 aas (Q6BGD8)
VatA9_1, 860 aas (Q3SDB6)
Vat beta subunit, 511 aas (Q3SEA2)
VhaA1/A2, 618 aas (Q4UJ82)
VhaC5/C6, 165 aas (Q4UJ88)
VhaF1, 127 aas (Q4UJ86)
subunit c of the H+-pumping V-type ATPase. Found to be essential for bloodstream-form Trypanosoma brucei through a genome-wide RNAi screen (Schmidt et al. 2018).
c-subunit of Trypanosoma brucei
H+-translocating A-type ATPase (Pisa et al., 2007b).
A-type ATPase of Methanosarcina mazei AhaABCDEFG
The A1A0-ATP synthase, Aha ABCDEFHIK or MbbrA1A0 (AhaC has 4 TMSs; each hairpin has a complete Na+-binding motif. Can use Na+ or H+ to synthesize ATP (McMillan et al., 2011).
Aha ABCDEFHIK of Methanobrevibacter ruminantium
Aha A (D3E1Z1)
Aha B (D3E1Z2)
Aha C (D3E1Y9)
Aha D (D3E1Z3)
Aha E (D3E1Y8)
Aha F (D3E1Z0)
Aha H (D3E1Y5)
Aha I (D3E1Y6)
Aha K (D3E1Y7)
Two sector V-type ATPase or ATP synthase of 12 subunits.
V-type ATPase of Treponema pallidum
AtpI1, AtpD1, AtpB1, AtpA1, NtpK, AtpD2, AtpB2, AtpA2, AtpF, NtpI2, plus two uncharacterized proteins.