Na⁺-, K⁺-ATPase (Na⁺ efflux; K⁺ uptake).  Kinetic alterations due to a missense mutation in the alpha2 subunit cause familial hemiplegic migraine type 2 (Segall et al. 2004). Mutation in the γ-subunit causes renal hypomagnesemia, associated with hypocalciurea (Cairo et al., 2008). The Na/K-ATPase is an important signal transducer that not only interacts and regulates protein kinases, but also functions as a scaffold (Li and Xie, 2009). Capsazepine, a synthetic vanilloid, converts the Na, K-ATPase to a Na-ATPase (Mahmmoud, 2008a). There are alternative α- and β-subunits, α₁, α₂,... β₁, β_2,... in muscle which form α₁β₁, α₁β₂, α₂β₁ and α₂β₂, heterodimers, each with differing Na⁺ affinities (4-13mM) (Kristensen and Juel, 2010). α₃ and β₃ isoforms have also been identified. The γ-subunit is the same as TC# 1.A.27.2.1. Poulsen et al. (2010) have proposed a second ion conduction pathway in the C-terminal part of the ATPase. The two C-terminal tyrosines stabilize the occluded Na/K pump conformations containing Na or K ions (Vedovato and Gadsby, 2010). Na⁺, K⁺-ATPase mutations causing familial hemiplegic migraines type 2 (FHM2) inhibit phosphorylation (Schack et al., 2012). Salt, the vascular Na⁺/K⁺ ATPase and the endogenous glycosides, ouabain and marinobufagenin, play roles in systemic hypertension (Hauck and Frishman, 2012). Protein kinase A (PKA) phosphorylation of Ser936 (in the intracellular loop between transmembrane segments M8 and M9) opens an intracellular C-terminal water pathway leading to the third Na⁺-binding site (Poulsen et al., 2012). PKA-mediated phosphorylation regulates activity in vivo. Ser-938 is located (Einholm et al. 2016). E960 on the Na⁺-K⁺-ATPase and F28 on phospholemman (PLM) are critical for phospholemman (PLM) inhibition, but there is at least one additional site that is important for tethering PLM to the ATPase. Mutations in the Na⁺/K⁺-ATPase α3 subunit gene (ATP1A3) cause rapid-onset dystonia-parkinsonism, a rare movement disorder characterized by sudden onset of dystonic spasms and slow movements (Doğanli et al. 2013).  The 3-d strcuture of the Na⁺-bound Na⁺,K⁺-ATPase at 4.3 Å resolution reveals the positions of the three Na⁺ ions (Nyblom et al. 2013).  Mutations cause adrenal hypertension (Kopec et al. 2014) as well as alternating hemiplegia of childhood (AHC) and rapid-onset dystonia- parkinsonism (RDP) (Rosewich et al. 2014).  Differences in the structures of the ouabain-, digonxin- and bufalin-bound enzyme have been reported (Laursen et al. 2015).  ATPase inhibitors have been shown to be effective anti-cancer agents (Alevizopoulos et al. 2014). Cys45 in the β-subunit can be glutathionylated, regulating the activity of the enzyme (Garcia et al. 2015). ATP1A2 mutations play a role in migraine headaches (Friedrich et al. 2016). The beta2 subunit is essential for motor physiology in mammals, and in contrast to beta1 and beta3, beta2 stabilizes the Na⁺-occluded E1P state relative to the outward-open E2P state (Hilbers et al. 2016). Numerous transcription factors, hormones, growth factors, lipids, and extracellular stimuli as well as epigenetic signals modulate the transcription of Na,K-ATPase subunits (Li and Langhans 2015). Čechová et al. 2016 have identified two cytoplasmic pathways along the pairs of TMSs, TMS3/TMS7 or TM6S/TMS9 that allow hydration of the cation binding sites or transport of cations from/to the bulk medium. Dissipation of the transmembrane gradient of K⁺ and Na⁺ due to ouabain inhibition increases Ptgs2 and Nr4a1 transcription by increasing Ca²⁺ influx through L-type Ca²⁺ channels that, in turn, leads to CaMKII-mediated phosphorylation of CREB and calcineurin-mediated dephosphorylation of NFAT, respectively (Smolyaninova et al. 2017). ZMay play a role in the development of gastric adenocarcinomas (Wang et al. 2017). Mutations F785L and T618M give rise to familial rapid onset dystonia parkonsonism by distinct mechanisms (Rodacker et al. 2006). Reacts with methylglyoxal to inhibit its activity (Svrckova et al. 2017).  Accumulation of beta-amyloid (Abeta) at the early stages of Alzheimer's disease is accompanied by reduction of Na,K-ATPase functional activity. Petrushanko et al. 2016 showed that monomeric Abeta(1-42) forms a tight (Kd of 3 mμM), enthalpy-driven equimolar complex with alpha1beta1 Na,K-ATPase. Complex formation results in dose-dependent inhibition of the enzyme hydrolytic activity. The binding site of Abeta(1-42) is localized in the "gap" between the α- and β-subunits of Na,K-ATPase, disrupting the enzyme functionality by preventing the subunits from shifting towards each other. Interaction of Na,K-ATPase with exogenous Abeta(1-42) leads to a pronounced decrease of the enzyme transport and hydrolytic activities and Src-kinase activation in neuroblastoma cells SH-SY5Y. This interaction allows regulation of Na,K-ATPase activity by short-term increases in the Abeta(1-42) level (Petrushanko et al. 2016). Two distinct phospholipids bind to two distinct sites on the ATPase, affecting activity and stability (Habeck et al. 2017). Five cysteinyl residues (C452, C456, C457, C577, and C656) serve as the cisplatin binding sites on the cytoplasmic loop connecting transmembrane helices 4 and 5 (Šeflová et al. 2018). Mutations can cause F/SHM with moderate penitrance (Prontera et al. 2018).  Arginine substitution of a cysteine in transmembrane helix M8 converts the Na⁺,K⁺-ATPase to an electroneutral pump similar to the gastric H⁺,K⁺-ATPase (Holm et al. 2017). Early onset life-threatening epilepsy can be associated with ATP1A3 gene variants (Ishihara et al. 2019), and loss of Na/K pump function is the common feature of mutants that induce hyperaldosteronism (Meyer et al. 2019). Three Na⁺ sites are defined in the Na⁺-bound crystal structure of the Na⁺, K⁺-ATPase. Sites I and II overlap with two K⁺ sites in the K⁺-bound structure, whereas site III is unique and Na⁺ specific. A glutamine in transmembrane helix M8 (Q925) appears from the crystal structures to coordinate Na⁺ at site III, but does not contribute to K⁺ coordination at sites I and II. Nielsen et al. 2019 addressed the functional role of Q925 in the various conformational states of this-ATPase by examining the mutants Q925A/G/E/N/L/I/Y both enzymatically and electrophysiologically, thereby revealing their Na⁺ and K⁺ binding properties. Q925 substitutions had minor effects on Na⁺ binding from the intracellular side of the membrane, but mutations Q925A and Q925G increased the apparent Na⁺ affinity, but caused dramatic reductions of the binding of K⁺ as well as Na⁺ from the extracellular side of the membrane. Thus, an interaction between sites III and I and a possible gating function of Q925 in the release of Na⁺ at the extracellular side are supported (Nielsen et al. 2019). The alpha2 Na⁺/K⁺-ATPase isoform mediates LPS-induced neuroinflammation (Leite et al. 2020). Apical periodontitis induces changes on oxidative stress parameters and increases Na⁺/K⁺-ATPase activity in adult rats (Barcelos et al. 2020). Familial hemiplegic migraine type 2 can be due to a missense mutation (L425H) in ATP1A2 (Antonaci et al. 2021). Mutations in ATP1A3 and FXYD genes (TC# 1.A.27) can cause childhood-onset schizophrenia (Chaumette et al. 2020). The ATPase plays a role in cell adhesion, motility, and migration of cancer cells (Silva et al. 2021). TMS2 moves outward as Na⁺ is deoccluded from the E1 conformation (Young and Artigas 2021). Kinetic properties and crystal structures of the Na⁺,K⁺-ATPase in complex with cardiotonic steroids (CTS) has revealed differences between CTS subfamilies. Ladefoged et al. 2021 found beneficial effects of K⁺ on bufadienolide binding in contrast to the well-known antagonism between K⁺ and cardenolides. Bufadienolide binding is affected by (i) electrostatic attraction of the lactone ring by a cation and (ii) the ability of a cation to stabilize and "shape" the site constituted by transmembrane helices of the alpha-subunit (αM1-6). The latter effect was due to varying coordination patterns involving amino acid residues from helix bundles αM1-4 and αM5-10. Substituents on the steroid core of a bufadienolide add to and modify the cation effects (Ladefoged et al. 2021). The Na⁺-K⁺-ATPase functions in the developing hippocampus (Shao et al. 2021). CryoEM analyses of the Na⁺,K⁺-ATPase in the two E2P states with and without cardiotonic steroids has revealed mechanistic details (Kanai et al. 2022). A conserved ion-binding site tyrosine plays a role in ion selectivity of the Na⁺/K⁺ pump (Spontarelli et al. 2022). Essential roles of the Na+K+-ATPase in ischemic pathology provide a platform for the improvement in clinical research on ischemic stroke (Zhu et al. 2022). In intact live cells, the regulatory complex is composed of two alpha subunits associated with two beta subunits, decorated with two PLM regulatory subunits. Docking and molecular dynamics (MD) simulations generated a structural model of the complex. alpha-alpha subunit interactions support conformational coupling of the catalytic subunits, which may enhance the NKA turnover rate (Seflova et al. 2022). There is a phenotypic continuum of ATP1A3-related disorders (Vezyroglou et al. 2022). The Na⁺/K⁺-ATPase is central to the pathogenesis of neurological diseases such as alternating hemiplegia of childhood. This ATPase has 3 distinct ion binding sites I-III. Binding of Na⁺ at each site in the human alpha3 Na⁺/K⁺-ATPase can be resolved using extracellular Na⁺-mediated transient currents. When the ATPase is constrained to bind and release only Na⁺, three kinetic components: fast, medium, and slow, can be isolated, depending on the voltage step direction and the occlusion (or deocclusion) of each of the 3 Na⁺s. Patient-derived mutations of residues which coordinate Na⁺ at site III exclusively impact the slow component, demonstrating that site III is crucial for deocclusion and release of the first Na⁺ into the extracellular milieu (Moreno et al. 2022). The opening of ion channels in cardiomyocytes is regulated by the surface electric double layer of the cell membrane as revealed by studies with digoxin (Zhou et al. 2022). The effects of H₂O₂ on cys residues and other targets in the Na,K-ATPase have been discussed (Chkadua et al. 2022). The influence of the Na⁺/K⁺-ATPase on neurodegenerative diseases has been reviewed (Zhang et al. 2022). The presence of two oppositely directed transmembrane ion gradients (for Na⁺ and K⁺) is important for robust stabilization of cellular volume in human erythrocytes (Ataullakhanov et al. 2022).  This ATPase plays important roles in neurodegenerative diseases (Zhang et al. 2022). Na/K-ATPase signaling tonically inhibits sodium reabsorption in the renal proximal tubule (Mukherji et al. 2023). Hypoxic stress-dependent regulation of Na,K-ATPase in ischemic heart disease has been reviewed (Baloglu 2023).  Chronic testosterone deficiency increases late inward sodium current and promotes triggered activity in ventricular myocytes from aging male mice (Banga et al. 2023). Three dynamic lipid interaction sites in the plasma membrane Na⁺,K⁺-ATPase influence activity of the transporter (Mahato and Andersson 2023). Interaction of pumps and transporters positioned at distant biological membranes with various forms of energy transfer between them may result in hypoxic/reperfusion injury, different kinds of muscle fatigue, and nerve-glia interactions (Dimitrov 2023). Marinobufagenin (MBG) is a member of the bufadienolide family of compounds, which are natural cardiac glycosides found in a variety of animal species, including man, which have different physiological and biochemical functions but have a common action on the inhibition of the Na⁺/K⁺-ATPase. MBG acts as an endogenous cardiotonic steroid, and in the last decade, its role as a pathogenic factor in various human diseases has emerged (Carullo et al. 2023).  A malfunctioning gene product is required for disease induction by ATP1A1 variants and that if a pathology is associated with protein-null variants, they may display low penetrance or high age of onset (Spontarelli et al. 2023). The Na,K-ATPase is a murzyme, facilitating thermodynamic equilibriums at the membrane-interface (Manoj et al. 2023).  The Na⁺K⁺-ATPase is present in boar sperm HPM, and it changes during capacitation (Awda et al. 2023). Clinical features of CAPOS syndrome are caused by maternal ATP1A3 gene variation (Gao et al. 2024).Inositol hexakisphosphate kinase 1 (IP6K1), governs the degradation of Na⁺/K⁺-ATPase via an autoinhibitory domain of PI3K p85α (Jin et al. 2024).  Two lysines in the transmembrane segments contribute to generate a pump with reduced stoichiometry (2 K⁺/1 Na⁺), allowing Artemia to maintain steeper Na⁺ gradients in hypersaline environments (Artigas et al. 2023).  Na⁺/K⁺-ATPase participates in Ca²⁺-signaling transduction and neurotransmitter release by coordinating the ion gradient across the cell membrane. This ATPase works synergistically with ion channels to form a dynamic network of ion homeostatic regulation and affects cellular communication (Huang et al. 2024).  Bufalin is a direct anticancer drug and a Na⁺/K⁺-ATPase inhibitor by forcing the Na⁺/Ca²⁺ exchanger to reverse its function, which transfers Ca²⁺ into the cytoplasm and ultimately causes Ca²⁺ overload-triggered pyroptosis (Li et al. 2024). Proximal tubule angiotensin II signaling regulates Na⁺ transporters in the mouse nephron (Nelson et al. 2021).  Aquaporin and the Na⁺/K⁺-ATPase are expressed in gill and gut cells of the shrimp Palaemon argentinus, regulated by ecdysone (Foguesatto et al. 2024).

Animals

3 component systems:
Na⁺-, K⁺-ATPase from α, β, γ heterotrimer of Homo sapiens
α₁ (ATP1A1) (P05023)
α₂ (ATP1A2) (P50993)
α₃ (ATP1A3) (P13637)
β₁ (ATP1B1) (P05026)
β₂ (ATP1B2) (Q58I19)
β₃ (ATP1B3) (P54709)
γ₁ (ATP1G1) (P54710)

Putative archaeal Na⁺, K⁺ ATPase, Mac8 (encoded with methylcobalamin: coenzyme M methyltransferase; methanol-specific, a metal chaparone protein and an electron transfer protein) (Chan et al., 2010).

Archaea

Putative Na⁺/K⁺ ATPase of Methanosarcina acetivorans (Q8THY0)

Na⁺,K⁺-ATPase α2 subunit, ATP1a2a or ATPA2A. Deficiency causes brain ventricle dilation and embryonic motility in zebra fish. Is essential for skeletal and heart muscle function (Doganli et al. 2012).

Animals

ATPA2 of Danio rerio (Q90X34)

Na⁺,K⁺-ATPase subunits α (837 aas) and β (302 aas) of the blood fluke ().

Animals (Platyhelminthes)

Na⁺,K⁺-ATPase subunits α and β of Schistosoma mansoni
alpha, G4VGA0
beta, G4VTH6

H⁺/K⁺-ATPase, ATP12A or ATP1AL1 of 1039 aas and 10 TMSs in a 2 + 2 + 6 TMS arrangement.  It plays a role in myocardial relaxation (Knez et al. 2014), but also functions in airway surface liquid acidification which impaires airway host defenses in cells lacking or compromised for CFTR (TC# 3.A.1.202.1) (Shah et al. 2016). This non-gastric H⁺/K⁺ ATPase (ATP12A) is expressed in mammalian spermatozoa (Favia et al. 2022) and may be sodium ion sensitive (Abe et al. 2023). Its cryoEM structures are known, and the mechanism has been explained (Abe et al. 2023), providing insight into the molecular mechanism of the E2-E1 transition and cooperative Na⁺-binding in the NKA and other related cation pumps. .

Animals

ATP12A of Homo sapiens

Na+/K+-ATPase of 1227 aas and 10 TMSs. Involved in cell signaling, volume regulation, and maintenance of electrochemical gradients (Morrill et al. 2016).  Genomic analyses of the euryhaline model ciliate Paramecium duboscqui reveal adaptations to environmental salinity via changes in transporter gene expression (Fu et al. 2024).

ATPase of Paramecium tetraurelia

Silkworm nerve Na⁺,K⁺-ATPase, α-subunit of 1009 aas and 10 TMSs (77% identical to the human ortholog). and the β-subunit of 326 aas and 1 TMS (30% identical to the human homolog). This ATPase, in contrast to mamalian ATPases, has high affinity for K⁺, but low affinity for Na⁺, suggesting that the β-subunit is responsible for the difference in Na⁺ affinity (Homareda et al. 2017).

Na⁺,K⁺-ATPase of Bombyx mori (domestic silkworm)

ATPase, Na+/K+ transporting subunit alpha 4, ATP1A4, of 1029 aas and 10 TMSs. Alternatively spliced transcript variants, encoding different isoforms, have been identified. ATP1A4 is exclusively expressed in germ cells and sperm and is essential for male fertility as it interacts with signaling molecules in both raft and non-raft fractions of the sperm plasma membrane to regulate capacitation-associated signaling, hyperactivation, sperm-oocyte interactions, and activation. ATP1A4 activity and expression increase during capacitation, challenging the widely accepted dogma of sperm translational quiescence (Tiwari et al. 2022).

ATP1A4 of Homo sapiens

H⁺-, K⁺-ATPase (gastric; H⁺ efflux; K⁺ uptake). Two H₃O⁺ may be transported per ATP hydrolyzed.  Howeve, a cryo-electron microscope structure suggests that 1 H⁺ and 1 K⁺ are transporter per ATP hydrolyzed, providing the energy needed to generate the one million fold H⁺ concentration gradient effected by this enzyme (Abe et al. 2012).  The detailed mechanism has been discussed, and the roles of essential residues have been proposed (Shin et al. 2011).  A number of inhibitors of acid secretion have been identified, and these are of pharmacological importance (Shin et al. 2011). The catalytic alpha subunit has ten transmembrane segments with a cluster of intramembranal carboxylic amino acids located in the middle of TMSs 4, 5, 6 and 8. The beta subunit has one TMS with the N terminus in the cytoplasm. The extracellular domain of the beta subunit contains six or seven N-linked glycosylation sites. N-glycosylation is important for enzyme assembly, maturation and sorting (Shin et al. 2009). The cryo-EM structure with bound BYK99, a high-affinity member of K⁺-competitive, imidazo[1,2-a]pyridine inhibitors, has been solved (Abe et al. 2017).

Animals

Gastric H⁺-, K⁺-ATPase from Homo sapiens

Non-gastric H⁺-, K⁺- or NH₄⁺-ATPase (Swarts et al., 2005; Worrell et al., 2008)

Animals

H⁺-, K⁺ or NH₄⁺-ATPase of Rattus norvegicus (P54708)

Spiny dogfish Na⁺,K⁺-ATPase (3-d structure solved at 2.4 Å resolution, Shinoda et al., 2009). The α-subunit is 88% identical to the human Na⁺,K⁺ ATPase (TC# 3.A.3.1.1).

Animals

Na⁺,K⁺-ATPase α, β, and γ subunits of Squalus acanthias
α (1028aas; Q4H132)
β (305aas; C4IX13)
γ (94aas; Q70Q12)

H⁺/K⁺-ATPase α-subunit (1534aas) (Ramos et al., 2011)

Fungi

H⁺/K⁺ ATPase of Aspergillus oryzae (Q2U3D2)

Putative Na⁺/K⁺-ATPase, Mhun_0636 (encoded in an operon with two half sized TrkA homologues, Mhun_0637 and Mhun_0638, that together may regulate the ATPase)

Archaea

Mhun_0636-8 of Methanospirillum hungatei
Mhun_0636 (Q2FLJ9) Mhun_0637 (Q2FLJ8) Mhun_0638 (Q2FLJ6)

Ouabain-insensitive K⁺-independent Na⁺-ATPase ɑ-subunit, AtnA; very similar to the human ɑ-1 chain of the Na⁺,K⁺-ATPase (3.A.3.1.1) (Rocafull et al., 2011).

Animals

AtnA of Cavia porcellus (B3SI05)

P-type ATPase 13a1 of 1193 aas

Plants

ATPase 13a1 of Ricinus communis (Castor bean)

Putative Mn²⁺-exporting P-type ATPase of 1343 aas.

Stramenopiles

ATPase of Albugo laibachii

This protein was reviously designated the functionally uncharacterized P-type ATPase 16 (FUPA16)  (Thever and Saier 2009).  Probable manganese exporter by similarity.

Alveolata (ciliates)

Putative Mn²⁺ ATPase of Tetrahymena thermophila (Q23QW3)

P-type ATPase with N-terminal MACPF domain (TC# 1.C.39) of 1982 aas

Ciliates

MACPF-Mn²⁺ P-type ATPase of Tetrahymena thermophila

This protein was previously designated the functionally uncharacterized P-type ATPase 17 (FUPA17) (Thever and Saier 2009), but it has been shown to be a Ca²⁺/Mn²⁺-exporting ATPase designated Cation-transporting ATPase 5 (Cta5 or ATP13A2) (Furune et al. 2008).

Yeast

ATPase of Schizosaccharomyces pombe (O14022)

This protein was previously designated the functionally uncharacterized P-type ATPase 18 (FUPA18 of 1491 aas) (Thever and Saier 2009).  It may be a Mn²⁺-ATPase (by similarity).

Alveolata

FUPA18a of Cryptosporidium parvum (Q5CW06)

This protein was previously designated the functionally uncharacterized P-type ATPase 19 (FUPA19 of 1807 aas) (Thever and Saier 2009).  The unusually large size and number of TMSs is unique to this protein.  Whether this is a consequence of an artifact of sequencing is not known.  It may be a Mn²⁺-ATPase (by similarity).

Alveolata

ATPase of Tetrahymena thermophilus

This protein was previously designated the functionally uncharacterized P-type ATPase 20 (FUPA20) (Thever and Saier 2009).  It may be a Mn²⁺-exporting ATPase (by similarity).

Alveolata (ciliates)

ATPase of Tetrahymena thermophila (Q22V52)

This protein was previously designated the functionally uncharacterized P-type ATPase 21 (FUPA21 of 1372 aas) (Thever and Saier 2009).  It may be a Mn²⁺-ATPase (by similarity).

Protozoan

ATPase of Thalassiosira pseudonana

This protein was previously designated the functionally uncharacterized P-type ATPase 22 (FUPA22 of 1212-2393 aas) (Thever and Saier 2009).  It may be a Mn²⁺-exporting ATPase (by similarity).

Alveolata

ATPase of Cryptosporidium parvum (Q5CTJ9)

Mn²⁺-exporting ATPase, ATP13A1 of 1204 aas.  Defects cause Mn²⁺-dependent neurological disorders.  Orthologous to the yeast Mn²⁺-ATPase, Spf1 (Cohen et al. 2013). It is present in the endoplasmic reticulum while the other P5 ATPases, A2 - A5, are in overlapping compartments of the endosomal system (Sørensen et al. 2018). It complements the yeast ER ATPase, SPF1 (TC#3.A.3.10.3) although ATP13A2 - 5 do not, and unlike these latter proteins, it seems to have 12 (rather than 10) TMSs, with the two extra ones in an N-terminal domain (Sørensen et al. 2018). ATP13A1 (Spf1 in yeast) directly interacts with the TMSs of mitochondrial tail-anchored proteins (McKenna et al. 2020). P5A-ATPase mediates the extraction of mistargeted proteins from the endoplasmic reticulum (ER). Cryo-electron microscopy structures of Saccharomyces cerevisiae Spf1 (TC# 3.A.3.10.3) revealed a large, membrane-accessible substrate-binding pocket that alternately faced the ER lumen and cytosol and an endogenous substrate resembling an alpha-helical TMS. Thus, the P5A-ATPase can dislocate misinserted hydrophobic helices flanked by short basic segments from the ER. TMS dislocation by the P5A-ATPase establishes an additional class of P-type ATPase substrates and may correct mistakes in protein targeting or topogenesis (McKenna et al. 2020). It has been designated as a transmembrane islocase (Dederer and Lemberg 2021). It was initially thought to mediate manganese transport (Cohen et al. 2013). However, it was later shown to specifically bind moderately hydrophobic TMSs with short hydrophilic lumenal domains that misinsert into the endoplasmic reticulum (McKenna et al. 2020). The P5A-ATPase extracts mistargeted or mis-inserted TMSs from the ER membrane for protein quality control, while the P5B-ATPases mediate export of polyamines from late endo-/lysosomes into the cytosol (Sim and Park 2023). ATP13A1 prevents ERAD of folding-competent mislocalized and misoriented proteins (McKenna et al. 2022). Thus, the P5A-ATPase ATP13A1 prevents the accumulation of mislocalized and misoriented proteins, which are eliminated by different ER-associated degradation (ERAD) pathways in mammalian cells. Without ATP13A1, mitochondrial tail-anchored proteins mislocalize to the ER through the ER membrane protein complex and are cleaved by signal peptide peptidase for ERAD. ATP13A1 also facilitates the topogenesis of a subset of proteins with an N-terminal TMS or a signal sequence that should insert into the ER membrane with a cytosolic N terminus. Without ATP13A1, such proteins accumulate in the wrong orientation and are targeted for ERAD by distinct ubiquitin ligases. Thus, ATP13A1 prevents ERAD of diverse proteins capable of proper folding (McKenna et al. 2022). The structure of Spf1 shows how it removes mislocated TA proteins (Sinning and McDowell 2022).  It  mediates a topogenesis pathway for folding multi-spanning membrane proteins (Ji et al. 2024).

Animals

ATP13A1 of Homo sapiens

Zebrafish ATP13A2 (Parkinson''s disease protein) is essential for embryonic survival (Lopes da Fonseca et al. 2013). A missense variant in Australian Cattle Dogs give rise to late onset neuronal ceroid lipofuscinosis (Schmutz et al. 2019).

Fish

ATP13A2 of Danio rerio (Q7SXR0)

Probable divalent cation transporting ATPase 13A4, ATP13A4, of 1196 aas and 10 TMSs. This protein had been suggested to be a Mg²⁺ transporter, but the evidence is equivocal (Schäffers et al. 2018). It may be a Mn²⁺/Ca²⁺ exporter. This protein as well as ATP13A2 has been implicated in Parkinson's disease and autism spectrum disorder (Sørensen et al. 2018). ATPA2 - 5 are all in compartments of the endosomal system and all have 10 TMSs with overlapping functions, often in different amounts in different tissues (Sørensen et al. 2018). Dysregulation of polyamine homeostasis strongly associates with human diseases. ATP13A2 is mutated in juvenile-onset Parkinson's disease and autosomal recessive spastic paraplegia 78. It is a transporter that balances the polyamine concentration between the lysosome and the cytosol. Single-particle cryo-EM solved high-resolution structures of human ATP13A2 in six intermediate states, including the putative E2 structure for the P5 subfamily of P-type ATPases. These structures comprise a nearly complete conformational cycle spanning the polyamine transport process and capture multiple substrate binding sites distributed along the transmembrane regions, suggesting a potential polyamine transport pathway (Mu et al. 2023).

ATP13A4 of Homo sapiens

Divalent cation transporting ATPase of 1207 aas and 9 putative TMSs, Catp-6.  C. elegans has three paralogues, Catp5, Catp6 and Catp7, with overlapping tissue expression patterns and functions (Zielich et al. 2018). 

Catp-5 of Caenorhabditis elegans

Manganese transporter of 1179 aas and 12 probable TMSs (Ticconi et al. 2004).  Mediates manganese transport into the endoplasmic reticulum. The ATPase activity is required for cellular manganese homeostasis. Plays an important role in pollen and root development through its impact on protein secretion and transport processes (Jakobsen et al. 2005). Functions together with LPR1 and LPR2 in a common pathway that adjusts root meristem activity to phosphate availability (Ticconi et al. 2009).

PDR2 of Arabidopsis thaliana (Mouse-ear cress)

Cation transporting P-type ATPase, ATP1, of 2400 aas

ATP1 of Plasmodium falciparum

Cation transporter, ATP3, of 2393 aas.

ATP3 of Plasmodium falciparum

Cation (Mn²⁺?) ATPase (ATP10) of 1918 aas

ATP10 of Plasmodium falciparum

The endoplasmic reticular ATPase, Spf1 or Cod1. PIt plays a role in ER Mn²⁺ homeostasis by pumping Mn²⁺ into the ER lumen (Cronin et al., 2002; Cohen et al. 2013). Deletion of the gene results in ER stress and lowered Mn²⁺ in the ER lumen (Cohen et al. 2013). This SPF1-ATPase is a transmembrane helix dislocase, used to remove some mislocated TM proteins from the outer membranes of mitochondria (McKenna et al. 2020). Spf1p exhibits unique structures at its N-terminus, including two putative additional transmembrane domains, and a large insertion connecting the P domain with transmembrane segment M5 (Petrovich et al. 2021). The Spf1p P5A-ATPase "arm-like" domain is not essential for ATP hydrolysis but its deletion impairs autophosphorylation (Grenon et al. 2021). Structures of this dismutase and Msp1 reveal how they remove mislocalized TA proteins from the ER and outer mitochondrial membranes, respectively (Sinning and McDowell 2022). ATP hydrolytic activity of purified Spf1p correlates with micellar lipid fluidity and is dependent on conserved residues in transmembrane helix M1. Free movement of the M1 helix represent an energetic constraint on catalysis, and this constraint is likely lost in the purified preparations, resulting in protein with intrinsic spontaneous ATP hydrolytic activity. Removal of the N-terminal part of the protein apparently removes this activity (Ipsen and Sørensen 2022). Inhibition of P5A-ATPases such as Spf1p could potentiate metal ion-induced ER stress and proteotoxicity (Petrovich et al. 2022).

Fungi

Spf1 of Saccharomyces cerevisiae (P39986)

P-type ATPase of 1308 aas

Alveolata

ATPase of Babesia equi

P-type ATPase of 1291 aas

Alveolata

ATPase of Cryptosporidium parvum

Putative Mn²⁺-exporting P-type ATPase of 1146 aas.

Microsporidia

APase of Encephalitozoon cuniculi (Q8SRH4)

This protein, ATP13A2 or P5A ATPase or ATP13A(1), was orginally designated the functionally uncharacterized P-type ATPase, FUPA13 (Thever and Saier 2009).  It is the Parkinson''s disease (PD) gene product, PARK9 (ATP13A2), and its defect gives rise to multiple abnormalities (Dehay et al. 2012).  It is similar to the incorrectly assigned manganese exporter in yeast, Ypk1 (TC# 3.A.3.10.8), and may have the same function, but in lysosomes, it is a polyamine (spermine/spermidine) exporter (van Veen et al. 2020). Toxic levels of manganese or abnormal levels of polyamines may cause a syndrome simiilar to PD (Chesi et al. 2012).  Manganese homeostasis in the nervous system has been reviewed (Chen et al. 2015).  The progression of PD may involve the lysosome and different autophagy pathways (Gan-Or et al. 2015).  It exhibits an activity-independent scaffolding role in trafficking/export of intracellular cargo in response to proteotoxic stress (Demirsoy et al. 2017). Mutations cause rare early onset Parkinson's disease (Suleiman et al. 2018). ATP13A2 modulates astrocyte-mediated neuroinflammation via NLRP3 inflammasome activation, thus bringing to light a direct link between astrocyte lysosomes and neuroinflammation in the pathological model of PD (Qiao et al. 2016). ATP13A2 and its close homologs, collectively known as P5B-ATPases, are polyamine transporters in endo-/lysosomes. Cryo-EM structures of human ATP13A2 in five distinct conformational intermediates, which together, represent a near-complete transport cycle of ATP13A2, have been determined. The structural basis of the polyamine specificity was revealed by an endogenous polyamine molecule bound to a narrow, elongated cavity within the transmembrane domain. The structures show an atypical transport path for a water-soluble substrate, in which polyamines may exit within the cytosolic leaflet of the membrane (Sim et al. 2021). Spermine is exported from the lysosome. The transmembrane domain serves as a substrate binding site, and the C-terminal domain is essential for protein stability and may play a regulatory role (Chen et al. 2021). The carcinogenic effects of ATP13A2 in different tumors has been studied (Zheng and Li 2021). High-resolution cryo-EM structures of human ATP13A2 in five distinct conformational intermediates have been determined, which together, represent a near-complete transport cycle of ATP13A2. The structural basis of the polyamine specificity was revealed by an endogenous polyamine molecule bound to a narrow, elongated cavity within the transmembrane domain. The structures show an atypical transport path for a water-soluble substrate, in which polyamines may exit within the cytosolic leaflet of the membrane (Sim et al. 2021). Mutations in ATP13A2 aare associated with mixed neurological presentations and iron toxicity due to nonsense-mediated decay (Kırımtay et al. 2021). The importance of the protein in regulating neuronal integrity has been established, and the structural dynamics and catalytic mechanism have been proposed (Mateeva et al. 2021). It is an ATPase which acts as a lysosomal polyamine exporter with high affinity for spermine, and also stimulates cellular uptake of polyamines and protects against polyamine toxicity (van Veen et al. 2020; Sim and Park 2023). Dysregulation of polyamine homeostasis strongly associates with human diseases. ATP13A2 is mutated in juvenile-onset Parkinson's disease and autosomal recessive spastic paraplegia 78. It is a transporter that balances the polyamine concentration between the lysosome and the cytosol. Single-particle cryo-EM solved high-resolution structures of human ATP13A2 in six intermediate states, including the putative E2 structure for the P5 subfamily of P-type ATPases. These structures comprise a nearly complete conformational cycle spanning the polyamine transport process and capture multiple substrate binding sites distributed along the transmembrane regions, suggesting a potential polyamine transport pathway (Mu et al. 2023).

Animals

PARK9 of Homo sapiens

This protein, P5B-ATPase, was originally designated the functionally uncharacterized P-type ATPase 14 (FUPA14) (Thever and Saier 2009), but it has been shown to be a vacuolar ATPase, Ypk1, that functions in manganese detoxification and homeostasis (Chesi et al. 2012).  It is therefore likely to catalyze export of manganese ions from the cytoplasm into the vacuole. However, it also transporter polyamines such as spermine . The 3-D structure has been determined to 3.4 Å, and it revealed three separate transport cycle intermediates, including spermine-bound conformations (Li et al. 2021). In the absence of cargo, Ypk9 rests in a phosphorylated conformation auto-inhibited by the N-terminus. Spermine uptake into vesicles is accomplished through an electronegative cleft lined by transmembrane segments 2, 4 and 6 (Li et al. 2021).

Fungi

Ypk1 of Saccharomyces cerevisiae (gi6324865)

This protein was previously designated the functionally uncharacterized P-type ATPase (FUPA15) (Thever and Saier 2009).  Probable manganese exporter by similarity (see 3.A.3.10.7 and 3.A.3.10.8).

Slime molds

Putative Mn²⁺-ATPase of Dictyostelium discoideum

Plasma membrane Ca²⁺-ATPase (efflux), PMCA4 (Giacomello et al. 2013).  The CD147 immunosupression protein interacts via its immunomodulatory domains with PMCA4 to bypass T-cell receptor proximal signaling and inhibit interleukin-2 (IL-2) expression (Supper et al. 2016). Deletion of residues 300 - 349, corresponding the the residues deleted in a natural splice variant (de Tezanos Pinto and Adamo 2006). The plasma membrane Ca²⁺ pump PMCA4z Is more active than splicing variant PMCA4x (Corradi et al. 2021).

Eukaryotes

Plasma membrane Ca²⁺-translocating ATPase, PMCA4, of Homo sapiens (P23634)

Endomembrane plasma membrane-type Ca²⁺ ATPase, ACA2 (Arabidopsis Ca²⁺ ATPase isoform 2) (lacks a C-terminal calmodulin domain, but activity is stimulated 5x by calmodulin which binds to an N-terminal inhibitory domain (Harper et al., 1998; Kamrul Huda et al. 2013).

Plants

ACA2 of Arabidopsis thaliana
(O81108)

Endoplasmic reticular (ER)-type Ca²⁺/Mn²⁺ ATPase, ECA1; 80% identical to and orthologous to the Medicago truncatula MCA8 protein of 1081 aas (F9W2W4). 42 P-type II Ca²⁺ ATPase genes have been found in Triticum aestivum. which may play roles in plant growth, development and signalling during abiotic and biotic stresses (Taneja and Upadhyay 2018).

Plants

ECA1 of Arabidopsis thaliana
(P92939)

Autoinhibited Ca²⁺ ATPase (ACA9) (expressed in pollen plasma membrane and required for male fertility), calmodulin-binding (Schiøtt et al., 2004).

Plants

ACA9 of Arabidopsis thaliana
(Q9LU41)

Endomembrane (Golgi) Ca²⁺/Mn²⁺-ATPase, ECA3 (one of 4 close paralogues in A. thaliana (Mills et al., 2008; Kamrul Huda et al. 2013). It has 998 aas and 10 TMSs in a 2 + 2 + 6 TMS arrangement. ECA3 localizes to the trans-Golgi apparatus and plays a role in response to Mn²⁺ deficiency with severe effects seen in an eca3 nramp1 (see TC# 2.A.55.2.4) nramp2 triple mutant under low Mn²⁺ supply. ECA3 plays a minor role in Mn-toxicity tolerance, but only when the cis-Golgi-localized MTP11 (TC# 3.A.3.2.19) is non-functional (Farthing et al. 2023).  The trans-Golgi-localized MTP10 plays a role in Mn²⁺-toxicity tolerance, but only in mutants when MTP8 and MTP11 are non-functional.

().

Plants

ECA3 of Arabidopsis thaliana (Q0WP80)

Ca²⁺-ATPase, Pmc1 (uptake into vacuoles) (Espeso 2016).

Yeast

Vacuolar membrane Ca²⁺-translocating ATPase from Saccharomyces cerevisiae Pmc1

Firmicutes

Cac1 of Clostridium acetobutylicum (Q97JK5)

Thermotogales

Pmo1 of Petrotoga mobilis (A9BJX0)

Firmicutes

Sth1 of Streptococcus thermophilus (Q5M0A4)

Putative Ca²⁺ ATPase most similar to Golgi Ca²⁺ ATPases of eukaryotes

Archaea

Putative Ca²⁺ ATPase of Methanococcus vannielii (A6URW9)

Putative Ca²⁺-ATPase (48% identical to 3.A.3.2.23) (like Golgi Ca²⁺-ATPases of eukaryotes)

Bacteria

Putative Ca²⁺-ATPase of Aguifex aeolicus (O66938)

Plasma membrane Ca²⁺-ATPase, isoform 1a (PMCA1) (78% identical to PMCA4 (TC# 3.A.3.2.1)). Maitotoxin converts it into a Ca²⁺-permeable nonselective cation channel (Sinkins et al., 2009). The C-terminal tail contains most of the regulatory sites including that for calmodulin. The pump is also regulated by acidic phospholipids, kinases, a dimerization process, and numerous protein interactors. In mammals, four genes code for the four basic isoforms. Isoform complexity is increased by alternative splicing of primary transcripts. Pumps 2 and 3 are expressed preferentially in the nervous system (Calì et al. 2017). This enzyme has two essential auxillary subunits, basigin and neuroplastin (NPTN), and the 3-d structure of the complex of PMCA1 with NPTN has been solved at 3.9 Å resolution (Gong et al. 2018). Methylene blue activates PMCA activity and cross-interacts with amyloid beta-peptide, blocking Abeta-mediated PMCA inhibition (Berrocal et al. 2018). Mutations leading to pathological neurooplastin (Np) variants, as exemplified by deafness causing Np mutants, can affect Np-dependent Ca²⁺ regulatory mechanisms and may potentially cause intellectual and cognitive deficits in humans (Liang et al. 2024).

Animals

PMCA1 of Homo sapiens (P20020)

The M535L virus Ca²⁺/Mn²⁺ efflux pump (transcribed during viral infection) (Bonza et al., 2010)

Virus

M535L Ca²⁺ pump of Paramecium bursaria chlorella virus, MT325 (A7IUR5)

Plasma Membrane Ca²⁺-type ATPase, NCA-2 (most like 3.A.3.2.2) (Bowman et al., 2011).

Fungi

NCA-2 of Neurospora crassa (Q9UUY2)

The probable Mg²⁺/Ca²⁺ ATPase antiporter (catalyzes Mg²⁺ uptake and Ca²⁺ efflux in a single coupled step; Neef et al. 2011)

Bacteria

Antiporter of Streptococcus pneumoniae (Q04JJ5)

The putative Ca⁺ ATPase with an extra C-terminal TMS followed by a lysin (LysM) domain of ~210aas. LysM domains are often found in cell wall degradative enzymes and have peptidoglycan binding sites. Found in Nitrosococcus oceani as well as Nitrosococcus halophilus. The ATPase domain is 46% identical to 3.A.3.2.4.

Bacteria

Putative Ca²⁺ ATPase of Nitrosococcus  halophilus (D5C355)

Ca²⁺-ATPase, Pmr1 (efflux) (also transport Mn²⁺ and Cd²⁺) (Lauer et al., 2008)

Eukaryotes

Golgi Ca²⁺-ATPase Pmr1 of Saccharomyces cerevisiae

Pleasma membrane Ca²⁺-ATPase of parenchymal tissue of the liver fluke, PMCA.  Interacts with a calmodulin-like protein, FhCaM1 in a calcium ion dependent fashion (Moore et al. 2012).

Animals

PMCA of Fasciola helpatica

Sarcoplasmic reticulum Ca²⁺ ATPase, Atp6.  The inhibitors, artemisinin and its anti-malarial derivatives, artesunate and artemether, bind to a hydrophobic pocket in a transmembrane region near the membrane surface (Naik et al. 2011; Meier et al. 2018). Other inhibitors include arterolane and thapsigargin (Meier et al. 2018).

Alveolata

Atp6 of Plasmodium falciparum

Lobster intracellular SERCA Ca²⁺ ATPase of 1020 aas.  In related species, expression of the gene is increased under hypersaline conditions, and the enzyme is ivolved in salinity stress adaptation (Wang et al. 2013).

animals (Arthropods)

ATPase of Palinurus argus

Crustacian plasma membrane calcium ATPase of 1170 aas (Chen et al. 2013).

Animals

Calcium ATPase of Callinectes sapidus (blue crab)

Ca²⁺/Mn²⁺-exporting ATPase, Pmr1 of 899 aas (Furune et al. 2008). It plays a role in the control of cell division involving Mn²⁺ sensitivity and the Cwh43 protein (see TC# 9.B.131.1.9 for details) (Nakazawa et al. 2019).

Yeast

Pmr1 of Schizosaccharomyces pombe

Calcium-exporting ATPase, Pmc1 of 1096 aas (Furune et al. 2008)..

Yeast

Pmc1 of Schizosaccharomyces pombe

SERCA Ca²⁺-ATPase of 1093 aas (Docampo et al. 2013).

Alveolata

SERCA ATPase of Toxoplasma gondii

SERCA P-type ATPase of 1036 aas.

Alveolata (Ciliates)

SERCA ATPase of Paramecium tetraurelia

Plasma membrane Ca²⁺ ATPase (PMCA) of 1146 aas (Plattner 2014).

Alveolata

PMCA of Paramecium tetraurelia

Plasma membrae Ca2+ ATPase (PMCA) of 1064 aas (Lescasse et al. 2005).

Alveolata (ciliates)

PMCA of Oxytricha trifallax (Sterkiella histriomuscorum)

Ca²⁺-ATPase of 905 aas and 10 TMSs, Pma1

Bacteria

Putative Ca²⁺-ATPase of Synechocystis sp. pMA1

Plasma membrane Ca²⁺ ATPase, isoform 2, of 1243 aas, ATP2b2.  The mouse orthologue, of 1198 aas (P9R0I7), when mutated (I1023S in TMS 10 and R561S in the catailytic core) gives rise to semi-dominant hearing loss (Carpinelli et al. 2013). Neuroplastin (TC# 8.A.23.1.8) expression is essential for hearing and hair cell PMCA expression (Lin et al. 2021).

Animals

ATP2b2 of Homo sapiens

P-type Na+-ATPase of 889 aas (Takemura et al. 2009).

Bacteria (Firmicutes)

Na+-ATPase of Exiguobacterium aurantiacum

Plasma membrane Ca²⁺-ATPase of 1033 aas, ACA12.  Can replace ACA9 which is normally required for male fertility.  ACA12 is not stimulated by calmodulin (Limonta et al. 2014).

Plants

ACA12 of Arabidopsis thaliana

SERCA1 of 1001 aas.  Several 3-D structures are known (e.g., 3W5B). One has an ATP analogue, a Mg²⁺ and two Ca²⁺ ions in the respective binding sites (Toyoshima and Mizutani 2004). In this state, the ATP reorganizes the three cytoplasmic domains (A, N and P), which are widely separated without nucleotide, by directly bridging the N and P domains. The structure of the P-domain itself is altered by the binding of the ATP analogue and Mg²⁺. As a result, the A-domain is tilted so that one of the TMSs moves to lock the cytoplasmic gate of the transmembrane Ca²⁺-binding sites. This appears to be the mechanism for occluding the bound Ca²⁺ ions, before releasing them into the lumen of the sarcoplasmic reticulum (Toyoshima and Mizutani 2004). Molecular dynamics simulations provided evidence for the role of the Mg²⁺ and K⁺ bound states in the transport mechanism (Espinoza-Fonseca et al. 2014).  Animal SERCAs are inhibited by three short single TMS membrane proteins, phospholamban (TC# 1.A.50.1), sarcolipin (1.A.50.2) and myoregulin (1.A.50.3), and the inhibitory actions of these peptides on SERCA are counteracted by a peptide called DWORF (Dwarf ORF) (Nelson et al. 2016; Anderson et al. 2015).  Norimatsu et al. 2017 have resolved the first layer of phospholipids surrounding the transmembrane helices. Phospholipids follow the movements of associated residues, causing local distortions and changes in thickness of the bilayer. The entire protein tilts during the reaction cycle, governed primarily by a belt of Trp residues, to minimize energy costs accompanying the large perpendicular movements of the transmembrane helices. A class of Arg residues extend their side chains through the cytoplasm to exploit phospholipids as anchors for conformational switching (Norimatsu et al. 2017). The human ortholog (O14983) is 96% identical to this rabbit enzyme.  These enzymes are inhibited by the fungal mycotoxins, cyclopiazonic acid and thapsigargin (Darby et al. 2016; Houdou et al. 2019). The human ortholog is 97% identical and is of the same length. The SERCA residue Glu340 mediates interdomain communication that guides Ca²⁺ transport (Geurts et al. 2020). The SERCA Ca²⁺-ATPase may serve as a calcium-sensitive membrane-endoskeleton sensor in the sarcoplasmic reticulum (Nakamura et al. 2021). The C-terminal proton release pathway is a functional element of SERCA which provides a mechanistic model for its operation in the catalytic cycle of the pump (Espinoza-Fonseca 2021).

Animals

SERCA of Oryctolagus cuniculus (rabbit)

Crayfish basolateral plasma membrane Ca²⁺-ATPase, PMCA, of 1190 aas (Wheatly et al. 2007). 80% identical to the human orthologue.

PMCA of Procambarus clarkii (Red swamp crayfish)

The calmodulin-sensitive plasma membrane Ca²⁺-ATPase (PMCA) of 1080 aas and 10 TMSs.  It has a non-canonical calmodulin (CaM) binding domain that contains a C-terminal 1-18 motif (Pérez-Gordones et al. 2017).

PMCA of Trypanosoma equiperdum

Ca²⁺-ATPase of 880 aas and 10 TMSs, Ca1.  Key intermediates have been identified; Ca²⁺ efflux is rate-limited by phosphoenzyme formation. The transport process involves reversible steps and an irreversible step that follows release of ADP and extracellular release of Ca²⁺ (Dyla et al. 2017).

Ca1 of Listeria monocytogenes

Putative Ca²⁺ P-type ATPase, TMEM94, of 1356 aas and 10 TMSs in the usual 2 + 2 + 6 TMS arrangement.  This protein is very distantly related to all other members of the 3.A.3.2 family within the P-type ATPase superfamily, and therefore may have a different or unique function (Zhang et al. 2018). It may functioin with NPC2 of 123 aas and 1 N-terminal TMS. ERMA (TMEM94) transports Mg²⁺ uptake in the endoplasmic reticulum (Vishnu et al. 2024).  The ER is a major Mg²⁺ compartment refilled by TMEM94.  ERMA uniquely combines a P-type ATPase domain and a GMN motif for _ERMg²⁺ uptake. A tyrosine residue is crucial for Mg²⁺ binding, and activity is a mechanism conserved in both prokaryotic (MgtB and MgtA) and eukaryotic Mg²⁺ ATPases. Cardiac dysfunction by haploinsufficiency, abnormal Ca²⁺ cycling in mouse Erma^+/- cardiomyocytes, and ERMA mRNA silencing in human iPSC-cardiomyocytes collectively define ERMA as an essential component of _ERMg²⁺ uptake in eukaryotes (Vishnu et al. 2024). 

TMEM94 of Homo sapiens

Sarco/endoplasmic reticulum Ca²⁺ ATPase of 1018 aas and 10 TMSs (Roegner et al. 2018).

SARCA of Callinectes sapidus

Sarcoplasmic reticular Calcium-ATPase of 993 aas and 10 TMSs. Elongation and contraction of scallop sarcoplasmic reticulum (SR): ATP Stabilizes Ca²⁺-ATPase crystalline array elongation of SR vesicles (Nakamura et al. 2022).

Ca²⁺-ATPase of Mizuhopecten yessoensis (Yesso scallop)

The Golgi Ca²⁺, Mn²⁺-ATPase, human SPCA1 or SPCA1a (secretory-pathway Ca²⁺-ATPases (SPCAs)), ATP2C1 or Hussy-28 (efflux) (the Hailey-Hailey disease protein) is involved in responses to Golgi stress, apoptosis and mid-gestational death (Okunade et al., 2007). SPCA1 transports Mn²⁺ from the cytosol into the Golgi lumen. Increasing Golgi Mn²⁺ transport increased cell viability upon Mn²⁺ exposure, supporting a role in the management of Mn²⁺-induced neurotoxicity (Mukhopadhyay and Linstedt, 2011). SPCA1 governs the stability of TMEM165 (TC# 2.A.106.2.2) in Hailey-Hailey disease (Roy et al. 2020). Loss of ATP2C1 leads to impaired Notch1 signalling; ATP2C1-loss could promote a mechanism by which NOTCH1 is endocytosed and degraded (Zonfrilli et al. 2023).  Six cryo-EM structures of hSPCA1 in a series of intermediate states have revealed its near-complete conformational cycle (Wu et al. 2023). With the aid of molecular dynamics simulations, these structures offer a clear structural basis for Ca²⁺ entry and release in hSPCA1. hSPCA1 undergoes unique conformational changes during ATP binding and phosphorylation compared to other well-studied P-type II ATPases. In addition, a conformational distortion of the Ca²⁺-binding site induced by the separation of transmembrane helices 4L and 6 unveiling a distinct Ca²⁺ release mechanism. A structure of the long-sought CaE2P state of P-type IIA ATPases provided insight into the Ca²⁺ transport cycle (Wu et al. 2023). Structures of human SPCA1a in the ATP and Ca²⁺/Mn²⁺-bound (E1-ATP) state and the metal-free phosphorylated (E2P) state at 3.1- to 3.3-Å resolutions (Chen et al. 2023). The structures revealed that Ca²⁺ and Mn²⁺ share the same metal ion-binding pocket with similar but notably different coordination geometries in the transmembrane domain, corresponding to the second Ca²⁺-binding site in sarco/endoplasmic reticulum Ca²⁺-ATPase (SERCA).

Animals

hSPCA1 of Homo sapiens

Plasma membrane calcium-transporting ATPase, ATP2B3, of 1220 aas and 10 TMSs. This 3ATP-driven Ca²⁺ ion pump is involved in the maintaining basal intracellular Ca²⁺ levels at the presynaptic terminals (Calì et al. 2015; Tauber et al. 2016). It uses ATP as an energy source to transport cytosolic Ca²⁺ ions across the plasma membrane to the extracellular compartment, and
may counter-transport protons.

ATP2B3 of Homo sapiens

Ca²⁺/Na⁺/H⁺-ATPase, ATP4, putative, of 1264 aas

ATP4 of Plasmodium falciparum

Putative Ca²⁺ ATPase, ATP9, of 1834 aas.

ATP9 of Plasmodium falciparum

CtpF, a probable Ca²⁺ ATPase of 905 aas and 10 TMSs in a 2 + 2 + 6 TMS arrangement.  Specific targeting to the Mycobacterium tuberculosis P-type ATPase membrane transporter, CtpF, by antituberculous compounds obtained by structure-based design, has been demonstrated (Santos et al. 2023).

CtpF of Mycobacterium tuberculosis

Cation-transporting P-type ATPase of 1016 aas and probably 10 TMSs (Gaschignard et al. 2024). 

P-type ATPase of Desulfobacteraceae bacterium

The sarco/endoplasmic reticulum Ca²⁺ -ATPase, SERCA2b or ATP2A2, is encoded by the ATP2A2 gene.  Mutatioins give rise to Darier''s disease; the spectrum of mutations have been related to patients' phenotypes (Ahn et al., 2003; Godic et al. 2010).  SERCA1 functions as a heat generator in mitochondria of brown adipose tissue (de Meis et al., 2006). It normally functions as a Ca²⁺:H⁺ antiporter (Karjalainen et al., 2007). Capsaicin converts SERCA to a Ca²⁺ non-transporting ATPase that generates heat, and is thus a natural drug that augments uncoupled SERCA, resulting in thermogenesis (Mahmmoud, 2008b). Oligomeric interactions of the N-terminus of sarcolipin with the Ca-ATPase have been documented (Autry et al., 2011), and these interactions also uncouple ATP hydrolysis from Ca²⁺ transport (Sahoo et al. 2015) resulting in thermogenesis.  TMS 11, absent in SERCA1a and SERCA2a, functions in regulation (Gorski et al. 2012). The bovine SERCA has also been crystallized (2.9 Å resolution; Sacchetto et al., 2012).  These enzymes are regulated differentially by phospholamban (PLN; 1.A.50.1.1) and sarcolipin (SLN; 1.A.50.2.1) as noted above (Gorski et al. 2013).  SERCA2 is regulated by TMEM64 (9.B.27.5.1), a 380 aa 6 TMS membrane protein of the DedA family (TC# 9.B.27) which regulates Ca²⁺ oscillations by direct interaction with CIRCA2, modulating its activity and influencing osteoblast differentiation (Kim et al. 2013).  Animal SERCAs are inhibited by three short single (C-terminal) TMS membrane proteins, phospholamban (TC# 1.A.50.1), sarcolipin (1.A.50.2) and myoregulin (1.A.50.3), and the inhibitory actions of these peptides on SERCA are counteracted by a peptide called DWORF (Dwarf ORF) (Nelson et al. 2016; Anderson et al. 2015). Small ankyrin 1 (sAnk1; TC#8.A.28.1.2) and sarcolipin (TC# 1.A.50.2.1) interact in their transmembrane domains to regulate SERCA (Desmond et al. 2017). Reduced SERCA function preferentially affects Wnt signaling by retaining E-cadherin in the endoplasmic reticulum and promotes apoptosis (Suisse and Treisman 2019). There is strong coupling between the chronological order of deprotonation, the entry of water molecules into the TM region, and the opening of the cytoplasmic gate. Deprotonation of E309 and E771 is sequential with E309 being the first to lose the proton. Deprotonation promotes the opening of the cytoplasmic gate but leads to a productive gating transition only if it occurs after the transmembrane domain has reached an intermediate conformation (Rui et al. 2018). Coordination at cation binding sites I and II is optimized for Ca²⁺ and to a lesser extent for Mg²⁺ and K⁺ (Sun et al. 2019). Methyglyoxal reacts with and inhibits SERCA (Zizkova et al. 2018). The phospholamban pentamer alters the function of SERCA (Glaves et al. 2019). TMS11 followed by the luminal tail is inhibitory. Inoue et al. 2019 determined the crystal structures of SERCA2b and its C-terminal splicing variant SERCA2a, both in the E1-2Ca²⁺-adenylylmethylenediphosphonate (AMPPCP) state. TMS11 is located adjacent to TMS10 and interacts weakly with a part of the L8/9 loop as well as the N-terminal end of TMS10, thereby inhibiting the SERCA2b catalytic cycle (Inoue et al. 2019). Accordingly, mutational disruption of the interactions between TMS11 and its neighboring residues caused SERCA2b to display SERCA2a-like ATPase activity. The authors proposed that TMS11 serves as a key modulator of SERCA2b activity by fine-tuning the intramolecular interactions with other transmembrane regions. Kabashima et al. 2020 revealed what ATP binding does to the Ca²⁺ pump and how nonproductive phosphoryl transfer is prevented in the absence of Ca²⁺. They reported that the A-domain takes an E1 position, and the N-domain occupies exactly the same position as that in the E1.ATP.2Ca²⁺ state relative to the P-domain. As a result, ATP is properly delivered to the phosphorylation site. Yet phosphoryl transfer never takes place without filling the two transmembrane Ca²⁺-binding sites. This explains what ATP binding does to SERCA, and how nonproductive phosphorylation is prevented in E2 (Kabashima et al. 2020). Nonannular lipid binding is not necessary for the stability of the E2 state but may become functionally significant during the E2-to-E1 transition (Espinoza-Fonseca 2019). Structural changes induced by the binding of rutin arachidonate to SERCA1a may shift proton balance near the titrable residues Glu771 and Glu309 into neutral species, hence preventing the binding of calcium ions to the transmembrane binding sites and thus affecting calcium homeostasis (Rodríguez and Májeková 2020). SERCA2a is a key protein in the Ca²⁺ cycle during heart failure (Zhihao et al. 2020). Covalent conjugates of fullerene derivatives with xanthene dyes inhibit SERCA (Tatyanenko et al. 2020). Autophosphorylation of the pump with two bound Ca²⁺ ions triggers a large conformational change that opens a gate on the luminal side of the membrane allowing the release of the ions. In response to phosphorylation, the cytoplasmic domains are partially reconfigured into an intermediate state on the path toward the E2 state with a closed luminal gate (Thirman et al. 2021). In preB cells, loss of SERCA2 leads to reduced V(D)J recombination kinetics due to diminished RAG-mediated DNA cleavage (Chen et al. 2021). A series of structural changes may accompany the ordered dissociation of ADP, the A-domain rotation, and the rearrangement of the transmembrane (TM) helices. The luminal gate then opens to release Ca²⁺ toward the SR lumen. Intermediate structures on the pathway are stabilized by transient sidechain interactions between the A- and P-domains. Lipid molecules between TM helices play a key role in the stabilization (Kobayashi et al. 2021). Structural bases for the conformational and functional regulation of human SERCA2b have been reported (Zhang and Inaba 2022). DWARF interacts with SERCA and phospholamban (PLB), counteracting the inhibitory effect of PLB on SERCA (Rustad et al. 2023). p300-mediated acetylation of SERCA2a is a critical post-translational modification that decreases the pump's function and contributes to cardiac impairment in heart failure (Gorski et al. 2023). Therapeutic approaches targeting SERCA2 and associated proteasomes might protect against Cd²⁺-induced cytotoxicity and renal injury (Li et al. 2023). SERCA2 phosphorylation at serine 663 is a key regulator of Ca²⁺ homeostasis in heart diseases (Gonnot et al. 2023).  The E protein of SARS-CoV-2 perturbes Ca²⁺ homeostasis. It is structurally similar to regulins such as phospholamban, that regulate the sarco/endoplasmic reticulum calcium ATPases (SERCA). The SARS-CoV-2 E protein affects SERCA as an exoregulin and forms oligomers with regulins, and thus alters the monomer/multimer regulin ratio thereby influencing their interactions with SERCAs. A direct interaction between E protein and SERCA2b results in a decrease in SERCA-mediated ER Ca²⁺ reload (Berta et al. 2024). Alarin regulates RyR2 and SERCA2 to improve cardiac function in heart failure with preserved ejection fraction (Li et al. 2024).

Animals

SERCA2b of Homo sapiens (P16615)

Ca²⁺-ATPase (efflux) with broad Ca²⁺ dependence (3.2-320 μm).  Probably inhibited by cipargamin and SJ1733 (Meier et al. 2018).

Protozoa

PfATPase4 of Plasmodium falciparum

Functionally uncharacterized P-type ATPase family 23 (FUPA23) (8 proteins from Actinomycetes; 650-802 aas) (Chan et al. 2010).

Actinobacteria

FUPA23a of Streptomyces coelicolor (Q9KXM5)

Cyanobacteria

FUPA23c of Trichodesmium erythraeum (Q10YH7)

Functionally uncharacterized P-type ATPase family 24 (FUPA24) (6 proteins of Actinomycetes; 760-1625 aas) (Chan et al. 2010).

Actinobacteria

FUPA24a of Mycobacterium bovis (Q7U2U7)

Functionally uncharacterized P-type ATPase family 24 (FUPA24) (1607aas); The first half is most like type I (Copper) ATPases, while the second half is most like type II ATPases (Ca²⁺).

Chloroflexi

FUPA24b of Thermomicrobium roseum (B9L3W5)

Functionally uncharacterized P-type ATPase family 24 (FUPA24) (1430aas)

δ-Proteobacteria

FUPA24c of Haliangium ochraceum (D0LKA4)

Functionally uncharacterized P-type ATPase family 24 (FUPA24) (1446aas)

γ-Proteobacteria

FUPA24d of Hahella chejuensis (ABC27339)

Functionally uncharacterized P-type ATPase family 25 (FUPA25.1) (4 proteins from Actinomycetes; 645-776 aas) (Chan et al. 2010).

Actinobacteria

FUPA25a of Streptomyces coelicolor (Q9RJ01)

P-type ATPase with a C-terminal hemeerythrin (Hr) domain (Traverso et al., 2010). The Hr domain binds two iron ions per monomer (a diiron center) and may provide a regulatory or more direct function in iron transport (Traverso et al., 2010).

Bacteria

P_1B-5- ATPase of Acidothermus cellulolyticus (A0LQU2)

Functionally uncharacterized P-type ATPase family 27 (FUPA27) (multiple proteins from α-, β- and γ- proteobacteria; 817-851aas) (Chan et al. 2010).

Proteobacteria

FUPA27a of Neisseria meningitidis (Q9JZI0)

Functionally uncharacterized P-type ATPase family 27 (FUPA27), Lbi2 (

Spirochetes

FUPA27b of Leptospira biflexa (B0STR2)

Functionally uncharacterized ε-proteobacteria P-type ATPase

ε-proteobacteria

FUPA27c of Nitratiruptor sp. SB155-2 (A6Q500)

The Cu²⁺ - ATPase, CtpA. Required for assembly of periplasmic and membrane embedded copper-dependent oxidases, but not for copper tolerance (Hassani, et al. 2010). Possibly CtpA delivers Cu²⁺ directly to the enzymes in the membrane rather than catalyzing transmembrane transport: similar to (3.A.3.27.1).

Bacteria

CtpA of Rubrivivax gelatinosus (Q5GCB0)

Cu⁺ export ATPase, CopA2; provides copper for cytochrome oxidase assembly (González-Guerrero et al. 2010; Raimunda et al. 2013).

Proteobacteria

CopA2 of Pseudomonas aeruginosa

Functionally uncharacterized P-type ATPase family 29 (FUPA29) (1 protein from a δ-proteobacterium, 798 aas) (Chan et al. 2010).

Proteobacteria

FUPA29a of Bdellovibrio bacteriovorus (Q6MK07)

Functionally uncharacterized P-type ATPase family 29 (FUPA29) (2 proteins from flavobacteria; 792-795)

Bacteroidetes

FUPA29b of Flavobacterium johnsoniae (A5FGV9)

Plamsa membrane proton-pumping ATPase, Pma1, of 1003 aas and 10 putative TMSs in a 2 + 2 + 6 TMS arrangement.  Leptosphaeria maculans, lacking this enzyme, displays a total loss of pathogenicity towards its host plant (Brassica napus). The mutant is unable to germinate on the host leaf surface and is thus blocked at the pre-penetration stage. Reduction in Pma1 activity may disturb the electrochemical transmembrane gradient, thus leading to conidia defective in turgor pressure generation on the leaf surface. L. maculans possesses a second plasma membrane H⁺-ATPase-encoding gene, termed pma2 (Remy et al. 2008).

Pma1 of Leptosphaeria maculans

Probable H⁺ pumping P-type ATPase of 1068 aas and 10 TMSs, PMA1 (Shan et al. 2006). PnPMA1 is differentially expressed during pathogen asexual development with a more than 10-fold increase in expression in germinated cysts, the stage at which plant infection is initiated, compared to vegetative or sporulating hyphae or motile zoospores.  PnPMA1 contains all the catalytic domains characteristic of H⁺-ATPases but also has a distinct domain of approximately 155 amino acids that forms a putative cytoplasmic loop between transmembrane domains 8 and 9 (Shan et al. 2006).

PMA1 of Phytophthora nicotianae

ATPase-7, AHA7, of 961 aas and 10 TMSs. 73% identical to AHA2 with which it shares function.  AHA7 is autoinhibited by a sequence present in the extracellular loop between transmembrane segments 7 and 8. Autoinhibition of pump activity is regulated by extracellular pH, suggesting negative feedback regulation of AHA7 during establishment of an H⁺ gradient. Restriction of root hair elongation is dependent on both AHA2 and AHA7, with each having different roles in this process (Hoffmann et al. 2018).

AHA7 of Arabidopsis thaliana (Mouse-ear cress)

The plasma membrane H⁺-ATPase, of 951 aas and 10 TMSs in a 2 + 2 + 6 TMS arrangement, plays a role in alleviating the phytotoxicity of imazethapyr in wheat. Auxin and DIMBOA (2,4-dihydroxy-7-methoxy-2H,1,4-benzoxazin-3(4H)one) may regulate plant growth trends and detoxification effects mediated by the PM H⁺-ATPase (Huang et al. 2024).

PM H⁺-ATPase of Triticum aestivum

Bacteria

MntA of Lactobacillus plantarum

Plasma membrane H⁺-ATPase, TbHA1 (912 aas) (3 isoforms are present in T. brucei) (Luo et al., 2006). This and another H+-ATPase, (UniProt acc # Q388Z3; 97% identical to TbHA1) have been found to be essential for bloodstream-form Trypanosoma brucei through a genome-wide RNAi screen (Schmidt et al. 2018).

Protozoan

TbHA1 of Trypanosoma brucei (AAP30857)

Plamsa membrane H⁺-ATPase, Pma1 (pumps protons out of the cell to generate a membrane potential and regulate cytosolic pH) (Liu et al., 2006; Petrov, 2009). TMSs 4,5,6 and 8 comprise the H⁺ pathway where essential and important residues have been identified (Miranda et al., 2010). Residues in the loop between TMSs 5 and 6 play roles in protein stability, function, and insertion (Petrov 2015).  Pma1 interacts with the plamsa membrane Cch1/Mid1 (1.A.1.11.10) to regulate its activity by influencing the membrane potential (Cho et al. 2016).  Asp739 and Arg811 are important residues for the biogenesis and function of the enzyme as H⁺ transport determinants (Petrov 2017). Pma1, is a P3A-type ATPase and the primary protein component of the membrane compartment of Pma1 (MCP). Like other plasma membrane H⁺-ATPases, Pma1 assembles and functions as a hexamer, a property unique to this subfamily of P-type ATPases. It has been unclear how Pma1 organizes the yeast membrane into MCP microdomains, or why it is that Pma1 needs to assemble into a hexamer to establish the membrane electrochemical proton gradient. Zhao et al. 2021 reported a high-resolution cryo-EM study of native Pma1 hexamers embedded in endogenous lipids. The Pma1 hexamer encircles a liquid-crystalline membrane domain composed of 57 ordered lipid molecules. The Pma1-encircled lipid patch structure likely serves as the building block of the MCP. At pH 7.4, the carboxyl-terminal regulatory α-helix binds to the phosphorylation domains of two neighboring Pma1 subunits, locking the hexamer in the autoinhibited state. The regulatory helix becomes disordered at lower pH, leading to activation of the Pma1 hexamer. The activation process is accompanied by a 6.7 A downward shift and a 40 degrees rotation of transmembrane helices 1 and 2 that line the proton translocation path. The conformational changes enabled the authors to propose a detailed mechanism for ATP-hydrolysis-driven proton pumping across the plasma membrane (Zhao et al. 2021). An ER-accumulated mutant of yeast Pma1 causes membrane-related stress to induce the unfolded protein response (Phuong et al. 2023).

Yeast

H⁺-ATPase of Saccharomyces cerevisiae (P05030)

Plasma membrane H⁺ ATPase, PMA1 or AHA1 of 949 aas ad 10 TMSs in a 2 + 2 + 6 TMS arrangement. Three isoforms, AHA1, 2 & 3, exhibit different kinetic properties (Palmgren and Christensen, 1994). Both the N- and C-termini are directly involved in controlling the pump activity (Ekberg et al., 2010). Methyl jasmonate elicits stomatal closure in many plant species including A. thaliana, and stomatal closure is accompanied by large ion fluxes across the plasma membrane.  These events appear to be mediated by AHA1 (Yan et al. 2015). It is involved in root nutrient uptake, epidermal stomatal opening, phloem sucrose loading and unloading, and hypocotyl cell elongation (Ding et al. 2021). Auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H⁺-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H⁺ influx, causing apoplast alkalinization (Li et al. 2021). Hydrogen sulfide improves salt tolerance through persulfidation of PMA1 in Arabidopsis (Ma et al. 2023). H₂S promotes the binding of PMA1 to the transcriptional growth-regulating factor 4 (GRF4) through persulfidation, and then activating PMA, thus improving the salt tolerance of Arabidopsis (Ma et al. 2023).

Plants

AHA1 of Arabidopsis thaliana
(P20649)

Plasma membrane H⁺ ATPase, AHA6 (binds 14-3-3 proteins induced by phosphorylation of Thr948, causing activation; preferentially expressed in pollen; Bock et al., 2006) (82% identical to 3.A.3.3.7).

Plants

AHA6 of Arabidopsis thaliana (Q9SH76)

Proton pumping ATPase, AHA2.  94% identical to AHA1 (3.A.3.3.7); generates the plasma membrane pmf.  Cation-binding pockets have been identified (Ekberg et al. 2010).  The pump has been reconstituted into "nanodiscs" in a functionally monomeric form (Justesen et al. 2013).  Regulated at the post-translation level by cis-acting auto-inhibitory domains, which can be relieved by protein kinase-mediated phosphorylation or binding of specific lipid species such as lysophospholipids (Wielandt et al. 2015).  Pumping is stochastically interrupted by long-lived (~100 seconds) inactive or leaky states. Allosteric regulation by pH gradients modulates the switch between these states but not the pumping or leakage rates (Veshaguri et al. 2016).  They dynamics of the pump have been examined (Guerra and Bondar 2015). AHA2 drives root cell expansion (Hoffmann et al. 2018). This protein is 81% identical to the barley (Hordeum vulgare) HA1 of 956 aas and 10 TMSs. Plasma membrane H⁺-ATPase (HA1 and HA2) activity and/or expression is important for regulating the activity of K⁺ transporters and channels under drought stress conditions (Cai et al. 2019). Herbivore exposure enhances A. nanus tolerance to salt stress by activating the jasmonic acid-signalling pathway, increasing plasma membrane H⁺-ATPase activity, promoting cytosolic Ca²⁺ accumulation, and then restricting K⁺ leakage and reducing Na⁺ accumulation in the cytosol (Chen et al. 2020).  Anionic phospholipids stimulate the proton pumping activity of AHA2 (Paweletz et al. 2023). Plasma membrane H⁺-ATPases play roles in mineral nutrition and crop improvement (Zeng et al. 2024).

Plants

Proton pumping ATPase of Arabidopsis thaliana

Functionally uncharacterized P-type ATPase family 30 (FUPA30) (4 proteins from α-, β- and δ-proteobacteria; 825-896 aas) (Chan et al. 2010).

Proteobacteria

FUPA30a of Bdellovibrio bacteriovorus (Q6MPD9)

Cyanobacteria

FUPA30d of Anabaena variabilis (Q3M5P5)

Functionally uncharacterized P-type ATPase family 31 (FUPA31) (3 proteins from γ-proteobacteria; 673-1068) (most closely related to FUPA32 homologues) (probably an active enzyme) (Chan et al. 2010).

Proteobacteria

FUPA31a of Methylococcus capsulatus (Q606V3)

Functionally uncharacterized P-type ATPase family 31 (FUPA31b) (probably a pseudogene). Bears a C-terminal domain of the EcsC family (see 3.A.1.143.1) not found in other P-type ATPases.

Proteobacteria

FUPA31b of Methylococcus capsulatus (Q606U9)

Functionally uncharacterized P-type ATPase family 32 (FUPA32) (multiple proteins from α-, β-, γ-, δ- and ε-proteobacteria (690-720 aas) (Chan et al. 2010).  The proteins in subfamily 3.A.3.32 may all be ferric iron uptake transporters as indicated by the characterized bacterial iron transport protein, FezB, included in TCDB under TC# 9.A.83.1.1 because it is reported to function with FezA, a 131 aa protein with a single N-terminal TMS.  This protein may prove to be an auxilliary protein for the FezB ATPase (see TC# 9.A.83.1.1) (Pi et al. 2023). Other FezAB systems have been characterized in Gram-negative bacterial (Pi et al. 2023).

Proteobacteria

FUPA32a of Azoarcus sp. EbN1 (Q5P8C0)

FezAB iron transport system where FezA is a membrane protein with 131 aas and 1 N-terminal TMS, and FezB is an ATPase of the P-type ATPase family (Pi et al. 2023). FezB has 699 aas and may have 8 TMSs. The function identified for this protein indicates that other members of subfamily 3.A.3.32 may transport ferric iron (Pi et al. 2023). To survive within their hosts, bacterial pathogens have evolved iron uptake, storage and detoxification strategies to maintain iron homeostasis. Three Gram-negative environmental anaerobes produce iron-containing ferrosome granules. The Gram-positive bacterium Clostridioides difficile is the leading cause of nosocomial and antibiotic-associated infections in the USA. C. difficile undergoes an intracellular iron biomineralization process and stores iron in membrane-bound ferrosome organelles containing non-crystalline iron phosphate biominerals. FezA and a P_1B6-ATPase transporter (FezB), repressed by both iron and the ferric uptake regulator, Fur, are required for ferrosome formation and play an important role in iron homeostasis during transition from iron deficiency to excess. Ferrosomes are often localized adjacent to cellular membranes as shown by cryo-electron tomography. Using two mouse models of C. difficile infection, Pi et al. 2023 demonstrated that the ferrosome system is activated in the inflamed gut to combat calprotectin-mediated iron sequestration and is important for bacterial colonization and survival during C. difficile infection.

FezAB of Clostridioides difficile

Heavy metal cation-transporting P-type ATPase, CtpC; MtaA; Rv3270; FUPA32.2 (718 aas with at least 8 TMSs in a 4 + 2 + 2 TMS arrangement. However, there may be additional TMSs. It is a high affinity, slow turnover, heavy metal transporting ATPase CtpC (Rv3270), which is required for virulence. It controls the Mn²⁺ cytoplasmic quota and is involved in the uploading of Mn²⁺ into secreted metalloproteins (Padilla-Benavides et al. 2013). It shows a preference for Mn²⁺, but Zn²⁺, Co²⁺ and Cu²⁺ can act as alternative substrates although at slower turnover rates (Padilla-Benavides et al. 2013). It mediates resistance to zinc poisoning. Boudehen et al. 2022 showed that zinc resistance also depends on a chaperone-like protein, PacL1 (Rv3269; TC# 8.A.201.1.1). PacL1 contains an N-terminal TMS, a cytoplasmic region with glutamine/alanine repeats and a C-terminal metal-binding motif (MBM). PacL1 binds Zn²⁺, but the MBM is required only at high zinc concentrations. PacL1 co-localizes with CtpC in dynamic foci in the mycobacterial plasma membrane, and the two proteins form high molecular weight complexes. Foci formation does not require flotillin or the PacL1 MBM. However, deletion of the PacL1 Glu/Ala repeats leads to loss of CtpC and sensitivity to zinc. Genes pacL1 and ctpC appear to be in the same operon, and homologous gene pairs are found in the genomes of other bacteria. PacL1 colocalizes and functions redundantly with other PacL orthologs in M. tuberculosis. Thus, PacL proteins may act as scaffolds that assemble P-ATPase-containing metal efflux platforms mediating bacterial resistance to metal poisoning (Boudehen et al. 2022).

Actinobacteria

CtpC of Mycobacterium tuberculosis (P0A503)

Firmicutes

FUPA32c of Clostridium bartiettii (A6NST6)

Spirochetes

FUPA32e of Treponema denticola (Q73QH0)

Euryarchaeota

FUPA32f of Methanobrevibacter smithii (A5UJX0)

Verrucomicrobia

FUPA32g of Akkermansia muciniphila (B2UR24)

Cyanobacteria

FUPA32h of Thermosynechococcus elongatus (Q8DL41)

Heavy metal translocating P-type ATPase, P1B ATPase, with an N-terminal CoBaHMA domain indicative of a heavy metal associated (HMA) domain (Gaschignard et al. 2024). It has 737 aas and 8 TMSs in a 4 + 2 + 2 TMS arrangement and is from a delta proteobacterium NaphS2.

P1B ATPase of a delta proteobacterium, Naph52

Mg²⁺/Ni²⁺-ATPase (uptake) of 902 aas and 10 TMSs in a 2 + 2 + 6 TMS arrangement.  The structure of the Mg²⁺ transporter MgtA, solved by single particle cryo-electron microscopy (cryo-EM), high resolution structures of both a homodimeric form (2.9 Å), the first for a P-type ATPase, and a monomeric form (3.6 Å). Each monomeric unit of MgtA displays a structural architecture that is similar to other P-type ATPases with a transmembrane domain and two soluble domains. The dimer interface consists of contacts between residues in adjacent soluble nucleotide binding and phosphotransfer regions of the haloacid dehalogenase (HAD) domain (Zeinert et al. 2024).

Bacteria

MgtA of Salmonella typhimurium

Mg²⁺ ATPase (1182 aas; 18-20 TMSs) with an N-terminal (residues 1-325) transmembrane domain of 8-10 TMSs; homologous to residues 493-791 in O53781 of Mycobacterium tuberculosis (TC# 2.A.1.3.43). Residues 257-318 hit TMSs 7 and 8 in FmtC (MrpF), TC#2.A.1.3.37 with a score of 8 e^-4. The last 3 TMSs of the N-terminal fused domain of 3.A.3.4.3 and 3.A.3.4.4 are homologous (e^-10) to the last 3 TMSs in 2.A.1.3.43. The N-terminal domain is homologous to the 8TMS domains of 9.B.3 family members.

Bacteria

Mg²⁺-ATPase of Pseudomonas stutzeri (F2N2Z6)

Mg²⁺ P-type ATPase (1195 aas; 18-20 TMSs) with an extra N-terminal 8-10 TMSs (residues 1-330). Similar to 3.A.3.4.3. The last 3 TMSs of the N-terminal fused domain to 3.A.3.4.3 and 3.A.3.4.4 are homologous (e^-10) to the last 3 TMSs in 9.A.30.2.1. The N-terminal domain is homologous to the 8TMS domains of 9.B.3 family members.

Bacteria

Mg²⁺-ATPase with N-terminal 8-10 TMS domain of ~300 residues of Azotobacter vinelandii (C1DHA2)

Uncharacterized Mg²⁺-ATPase, MgtA, of 912 aas and 10 TMSs (Pohland and Schneider 2019).

MgtA of Microcystis aeruginosa

Cu⁺ (Km 0.3 μM), Ag⁺ transporting ATPase, CopB (Mana-Capelli et al., 2003)

Euryarchaea

CopB of Archaeoglobus fulgidus (AAB91079)

Chloroplast envelope Cu⁺-uptake ATPase, PAA1 or HMA1.  Essential for growth under adverse light conditions (Seigneurin-Berny et al. 2006).

Plants

PAA1 of Arabidopsis thaliana (Q9SZC9)

Chloroplast thylakoid Cu⁺-ATPase, PAA2/HMA8 (delivers Cu⁺ to the thylakoid lumen).  Degraded by the Clp protease undeer conditions of Cu⁺ excess (Tapken et al. 2014).

Plants

PAA2 of Arabidopsis thaliana (AAP55720)

The archaeal Cu⁺ efflux pump (CopA)

Archaea

CopA of Sulfolobus solfataricus (Q97UU7)

The transferable, plasmid-localized, copper sensitivity (uptake) ATPase, TcrA (811aas) (46% identical to 3.A.3.5.1) (Hasman, 2005)

Bacteria

TcrA of Enterococcus faecium (ABA39707)

The transferable, plasmid-localized, copper resistance (efflux) ATPase, TcrB (50% identical to 3.A.3.5.2) (Hasman, 2005)

Bacteria

TcrB of Enterococcus faecium (AAL05407)

Golgi Cu²⁺ ATPase, Ccc2, retrieves Cu²⁺ from the metallochaperone Atx1 and transports it to the lumen of Golgi vesicles (Lowe et al., 2004)

Yeast

Ccc2 of Saccharomyces cerevisiae
(P38995)

The copper resistance ATPase, CopA (Ettema et al., 2006; Lübben et al., 2007; Villafane et al., 2009).

Bacteria

CopA of Bacillus subtilis (O32220)

Cu⁺-, Ag⁺-ATPase (efflux). 

Bacteria

CopB of Enterococcus hirae

Crenarchaeota

PacS of Sulfolobus solfataricus (Q97VH4)

Crenarchaeota

Pae1 of Pyrobaculum aerophilum (Q8ZUJ0)

Euryarchaeota

Tro1 of Thermoplasma volcanium (Q978Z8)

Putative Copper P-type ATPase (46% identical to 3.A.3.5.10)

Korarchaea

Putative Copper P-type ATPase of Candidatus Korarchaeum cryptofilum (B1L487)

Crenarchaeota

Ape2 of Aeropyrum pernix (Q9YBZ6)

The copper (Cu²⁺) transporting ATPase, Ccc2

Yeast

Ccc2 of Schizosaccharomyces pombe (O59666)

Cu⁺-, Ag⁺-ATPase (efflux from the cytosol into the secretory pathway) (Barnes et al., 2005); ATP7B (Wilson's disease protein, α-chain) is continuously expressed in Purkinje neurons. It delivers Cu⁺ to the ferroxidase, ceruloplasmin, in liver and may also transport Fe²⁺ (Takeda et al., 2005). Critical roles for the COOH terminus of ATP7B in protein stability, trans-Golgi network retention, copper sensing, and retrograde trafficking have been reported (Braiterman et al. 2011).  Modeling suggests that Cu⁺-binding sites HMBDs 5 and 6 are most important for function (Gourdon et al. 2012).  ATP7B loads Cu⁺ into newly synthesized cupro-enzymes in the trans-Golgi network and exports excess copper out of cells by trafficking from the Golgi to the plasma membrane.  Mutations causing disease can affect activity, stability or trafficking (Braiterman et al. 2014).  Cisplatin is a poor substrate relative to Cu⁺with a Km of 1 mμM, and copper and cisplatin compete with each other (Safaei et al. 2008). Veratridine can bind to a site at the mouth of the channel pore in the human cardiac sodium channel, NaV1.5 (Gulsevin et al. 2022). ATP7A/B contains a P-type ATPase core consisting of a membrane transport domain and three cytoplasmic domains, the A, P, and N domains, and a unique amino terminus comprising six consecutive metal-binding domains. Bitter et al. 2022 presented a cryo-EM structure of frog ATP7B in a copper-free state. Interacting with both the A and P domains, the metal-binding domains are poised to exert copper-dependent regulation of ATP hydrolysis coupled to transmembrane copper transport. A ring of negatively charged residues lines the cytoplasmic copper entrance that is presumably gated by a conserved basic residue sitting at the center. Within the membrane, a network of copper-coordinating ligands delineates a stepwise copper transport pathway. Copper binding leads to increased dynamics in the regulatory N-terminal domain of ATP7B (Orädd et al. 2022). P-type ATPases follow an alternating access mechanism, with inward-facing E1 and outward-facing E2 conformations. Salustros et al. 2022 presented structures that reach 2.7 Å resolution of a copper-specific P1B-ATPase in an E1 conformation, with complementing data and analyses. A domain arrangement that generates space for interaction with ion-donating chaperones, suggests direct Cu⁺ transfer to the transmembrane core. A methionine serves a key role by assisting the release of the chaperone-bound ion and forming a cargo entry site together with the cysteines of the CPC signature motif. Yang et al. 2023 presented cryo-EM structures of human ATP7B in the E1 state in the apo, the putative copper-bound, and the putative cisplatin-bound forms. In ATP7B, the N-terminal sixth metal-binding domain (MBD6) binds at the cytosolic copperentry site of the transmembrane domain (TMD), facilitating the delivery of copper from the MBD6 to the TMD. The sulfur-containing residues in the TMD of ATP7B mark the copper transport pathway. By comparing structures of the E1 state of human ATP7B with the E2-P(i) state of frog ATP7B, an ATP-driving copper transport model was proposed (Yang et al. 2023).  A single ATP7 gene is present in non-chordate animals while it is divided into ATP7A and ATP7B in chordates (Fodor et al. 2023). Mutation in ATP7B can give rise to multiple neurological abnormalities without hepatic involvement (Kumar et al. 2024). Psychiatric symptoms in Wilson's Disease have been reviewed (Gromadzka et al. 2024).

Eukaryotes

Cu⁺-ATPase, ATP7B, of Homo sapiens

Copper (Cu⁺) exporting P-ATPase, CopA (3-D structure known to 3.2 Å; PDB# 3RFU; Gourdon et al. 2011).  The internal surface of the ATPase interacts with the copper chaparone, CopZ (Padilla-Benavides et al. 2012).  A sulfur-lined metal transport pathway has been identified (Mattle et al. 2015).  Cu⁺ is bound at a high-affinity transmembrane-binding site in trigonal-planar coordination with the Cys residues of the conserved CPC motif of transmembrane segment 4 (C382 and C384) and the conserved Methionine residue of transmembrane segment 6 (M717 of the MXXXS motif). These residues are also essential for transport (Mattle et al. 2015).

Bacteria

CopA of Legionella pneumophila (Q5X2N1)

Mycobacterial copper transporter, MctB (Wolschendorf et al., 2011).

Bacteria

MctB of Mycobacterium abscessus (B1MHH7)

Copper-transporting ATPase RAN1 or HMP7 (EC 3.6.3.4) (Protein HEAVY METAL ATPASE 7) (Protein RESPONSIVE TO ANTAGONIST 1). Receptors involved in ethylene signaling can acquire their copper load by different routes and adopt the metal ion from the plasma membrane either by sequential transfer from soluble chaperones of the ATX1-family via the ER-bound copper-transporting ATPase RAN1 or by direct transfer from the soluble chaperones (Hoppen and Groth 2020). ER-anchored SPL7 (Transcription factor) constitutes a cellular mechanism for the regulation of RAN1 in ethylene signaling and lays the foundation for investigating how Cu homeostatic conditions ethylene sensitivity in the developmental context (Yang et al. 2022).

Plants

RAN1 of Arabidopsis thaliana

Ca²⁺ exporting ATPase, CopA. The domain organization and mechanism have been studied (Hatori et al., 2009, Hatori et al., 2008, Hatori et al., 2007).  Residues involved in catalysis have been defined (Hatori et al. 2009).

Bacteria

CopA of Thermotoga martima (Q9WYF3)

Cu⁺ export ATPase, CopA1, required to maintain cytoplasmic copper levels (González-Guerrero et al. 2010; Raimunda et al. 2013).

Proteobacteria

CopA1 of Pseudomonas aeruginosa

Functionally uncharacterized P-type ATPase.  Three proteins from Corynebacteria of 841-976 aas are similar in sequence.  Formerly members of the FUPA26 family (Chan et al. 2010).

Actinobacteria

Uncharacterized ATPase of Corynebacterium diphtheriae (Q6NJJ6)

Functionally uncharacterized P-type ATPase, formerly of family 28 (FUPA28).  Two proteins in γ-proteobacteria are similar in sequence; of 847-852 aas (Chan et al. 2010).

Proteobacteria

P-type ATPase (formerly FUPA28a) of Legionella pneumophila (Q5ZYY0)

Copper exporting ATPase, ATP7 of 1254 aas and 10 - 12 TMSs.  DmATP7 is the sole Drosophila melanogaster ortholog of the human MNK and WND copper transporters. A regulatory element drives expression in all neuronal tissues examined and demonstrates copper-inducible, Mtf-1-dependent expression in the larval midgut. Thus, an important functional role for copper transport in neuronal tissues is implied. Regulation of DmATP7 expression is not used to limit copper absorption under toxic copper conditions. The protein localizes to the basolateral membrane of DmATP7 expressing midgut cells, supporting a role in export of copper from midgut cells (Burke et al. 2008).

ATP7 of Drosophila melanogaster (Fruit fly)

Cuprous ion (Cu⁺) exporter, CopB, of 785 aas and 8 TMSs in a 4 + 2 + 2 arrangement. The copper-transporting P1B-ATPases have been divided traditionally into two subfamilies, the P1B-1-ATPases or CopAs and the P1B-3-ATPases or CopBs. CopAs selectively export Cu⁺ whereas previous studies have suggested that CopBs are specific for Cu²⁺ export. Biochemical and spectroscopic characterization of Sphaerobacter thermophilus CopB (StCopB) showed that, while it does bind Cu²⁺, the binding site is not in the transmembrane domain (Purohit et al. 2018).  StCopB exhibits metal-stimulated ATPase activity in response to Cu⁺, but not Cu²⁺, indicating that it is actually a Cu⁺ transporter. Cu⁺ is coordinated by four sulfur ligands derived from conserved cysteine and methionine residues. The histidine-rich N-terminal region is required for maximal activity, but is inhibitory in the presence of divalent metal ions. P1B-1- and P1B-3-ATPases may therefore all transport Cu⁺ (Purohit et al. 2018).

CopB of Sphaerobacter thermophilus

Cu⁺, Zn²⁺, Cd²⁺ exporting ATPase of 815 aas and 8 TMSs, CueA. Has two N-terminal metal binding domains that are essential for resistance to these three metal ions (Liang et al. 2016).

CueA of Bradyrhizobium liaoningense

Ag⁺-ATPase (efflux) of 824 aas and 9 TMSs in a 5 + 2 + 2 TMS arrangement.

Bacteria

Ag⁺-ATPase, SilP of Salmonella typhimurium

Copper-exporting P-type ATPase of 742 aas and 8 TMSs (Singh et al. 2015).

CopA of Streptococcus mutans

Cuprous ion (Cu⁺) exporter, CtpA (does not export Co²⁺, Mn²⁺, Ni²⁺, Zn²⁺ or Cu²⁺).  K_m for Cu⁺ = 0.05 μM (León-Torres et al. 2015). 

Cu⁺ ATPase of Mycobacterium tuberculosis

Copper (Cu⁺) exporting ATPase of 1254 aas and 8 TMSs, CrpA. While the A. flavus protein has not been characterized at the date of this entry, the A. fumigatus ortholog has been (Werner et al. 2023). Cellular responses used by macrophages to counteract fungal infection is the accumulation of high phagolysosomal Cu levels to destroy ingested pathogens. A. fumigatus responds by activating high expression levels of crpA, which encodes a CrpA that actively transports excess Cu⁺ from the cytoplasm to the extracellular environment (Werner et al. 2023). Deletion of CrpA fungal-unique amino acids 1-211, containing two N-terminal Cu-binding sites, moderately increased Cu-sensitivity but did not affect expression or localization to the ER and cell surface. Replacement of CrpA fungal-unique amino acids 542-556, consisting of an intracellular loop between the second and third TMSs resulted in ER retention of the protein and strongly increased Cu-sensitivity (Werner et al. 2023).