2.A.36 The Monovalent Cation:Proton Antiporter-1 (CPA1) Family

The CPA1 family is a large family of proteins derived from Gram-positive and Gram-negative bacteria, blue-green bacteria, archaea and eukaryotes including yeast, plants and animals. Transporters from eukaryotes have been functionally characterized, and all of these catalyze Na+:H+ exchange. Their primary physiological functions may be in (1) cytoplasmic pH regulation, extruding the H+ generated during metabolism, and (2) salt tolerance (in plants), due to Na+ uptake into vacuoles. Bacterial homologues are also Na+:H+ antiporters, but some also catalyze Li+:H+ antiport or Ca2+:H+ antiport under some conditions (Waditee et al., 2001).  The pathophylsiology of human members of this family have been reviewed (Padan and Landau 2016). Most prokaryotic Na+/H+ exchangers belong to the Cation/Proton Antiporter (CPA) superfamily, the Ion Transport (IT) superfamily, or the Na+-translocating Mrp transporter superfamily (Patiño-Ruiz et al. 2022). Transport mechanisms for Na+/H+ exchangers that explain their highly pH-regulated activity profiles have been considered (Patiño-Ruiz et al. 2022). Dwivedi and Mahendiran 2022 describe the interplay in the structure-function of membrane transporter proteins that may be implemented to explore the plethora of biological events such as conformation, folding, ion binding and translocation.

The phylogenetic tree for the CPA1 family shows three principal clusters. The first cluster includes proteins derived exclusively from animals, and all of the functionally characterized members of the family belong to this cluster. Of the two remaining clusters, one includes all bacterial homologues while the other includes one from Arabidopsis thaliana, one from Homo sapiens and two from yeast (S. cerevisiae and S. pombe). Several organisms possess multiple paralogues; for example seven paralogues are found in C. elegans, and five are known for humans. Most of these paralogues are very similar in sequence, and they belong to the animal specific cluster.

Using the mammalian NHE1 (2.A.36.1.1), it has been found that TMSs 4 and 9 as well as the extracellular loop between TMSs 3 and 4 are important for drug (amiloride- and benzoyl guanidinium-based derivatives) sensitivities. Mutations in these regions also affect transport activities. M4 and M9 therefore contain critical sites for both drug and cation recognition. Cation/proton antiporters (CPAs) regulate cells' salt concentrations and internal pH. Their malfunction is associated with a range of human pathologies, yet only a handful of CPA-targeting therapeutics are presently in clinical studies. Masrati et al. 2023 discussed how recently published mammalian protein structures and emerging computational technologies may help to bridge this gap.

Daxx, a death domain-associated protein, (O35613) interacts with sodium hydrogen exchanger isoform 1 (NHE1). During ischemic stress, Daxx translocates from the nucleus to the cytoplasm, where it colocalizes with NHE1. Daxx binds to the ezrin/radixin/moesin (ERM)-interacting domain of NHE1, in competition with ezrin. Ischemic insult may trigger the nucleo-cytoplasmic translocation of Daxx, following which cytoplasmic Daxx stimulates the NHE1 transporter activity and suppresses activation of the NHE1-ezrin-Akt-1 pathway (Jung et al., 2007).

One homologue, Nhe (TC #2.A.36.1.4), is a chloride-dependent Na+:H+ antiporter in which residues 1-375 of the 438 aas are identical to Nhe-1 (TC #2.A.36.1.1). The C-terminal 63 residues are unique (Sangan et al., 2002). It is found in the apical membranes of crypt cells of the rat distal colon. This protein was reported to exhibit 6 putative TMSs and is encoded by a 2.5 kb mRNA present in many tissues (Sangan et al., 2002). However, the WHAT program predicts 10 TMSs. nhe transfected fibroblasts exhibit Cl--dependent Na+-dependent intracellular pH recovery to an acid load that was blocked by 5-ethylisopropylamiloride and 5'-nitro-2-(3-phenylpropylamino)benzoate (a Cl- channel blocker).

Numerous members of the CPA1 family have been sequenced, and these proteins vary substantially in size. The bacterial proteins have 527-549 amino acyl residues while eukaryotic proteins are generally larger, varying in size from 541-894 residues. They exhibit 10-12 putative transmembrane α-helical spanners (TMSs). A proposed topological model (Wakabayashi et al., 2000) suggests that in addition to 12 TMSs, a region between TMSs 9 and 10 dips into the membrane to line the pore. However, one homologue, Nhx1 of S. cerevisiae, has an extracellular glycosylated C-terminus (Wells and Rao, 2001).

A gene encoding a Na+/H+ antiporter was cloned from the chromosome of Halobacillus dabanensis strain D-8(T) by functional complementation. Its presence enabled the antiporter-deficient E. coli strain KNabc to survive in the presence of 0.2 M NaCl or 5 mM LiCl (Yang et al. 2006). The gene was sequenced and designated as nhaH (2.A.36.6.7). NhaH has 403 residues and is 54% identical and 76% similar to the NhaG Na+/H+ antiporter of Bacillus subtilis (TC# 2.A.36.6.2). The hydropathy profile was characteristic of a membrane protein with 12 putative transmembrane domains. Everted membrane vesicles prepared from E. coli cells carrying nhaH exhibited Na+/H+ as well as Li+/H+ antiporter activity, which was pH-dependent with highest activities at pH 8.5-9.0 and at pH 8.5, respectively. nhaH confers upon E. coli KNabc cells the ability to grow under alkaline conditions (Yang et al., 2006). 

Na+, K+ and pH homeostasis are controlled by the monovalent cation proton antiporter (CPA) superfamily. Kong et al. 2021 identified 35 ZmCPAs in maize comprising 13 Na+/H+ exchangers (ZmNHXs), 16 cation/H+ exchanger (ZmCHXs), and 6 K+ efflux antiporters (ZmKEAs). Most of them were localized to the plasma membrane or tonoplast. ZmCHXs were highly expressed in anthers, while ZmNHXs and ZmKEAs showed high expression in various tissues. ZmNHX5 and ZmKEA2 were up-regulated in maize seedlings under both NaCl and KCl stresses. Yeast complementation experiments revealed the roles of ZmNHX5, ZmKEA2 in NaCl tolerance (Kong et al. 2021).

Membrane ion channels and Na+-Li+/H+ exchangers (NHEs) fractionate Li isotopes (Poet et al. 2023). This systematic 6Li enrichment is driven by the membrane potential for channels, and by intracellular pH for NHEs, where it displays cooperativity, a hallmark of dimeric transport, evidencing that transport proteins discriminate between isotopes differing by one neutron.

The generalized transport reaction catalyzed by functionally characterized members of the CPA1 family is:

Na+ (out) + H+ (in) ⇌ Na+ (in) + H+ (out)

This family belongs to the CPA Superfamily.



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Patiño-Ruiz, M., C. Ganea, and O. Călinescu. (2022). Prokaryotic Na/H Exchangers-Transport Mechanism and Essential Residues. Int J Mol Sci 23:.

Pfeiffer, J., D. Johnson, and K. Nehrke. (2008). Oscillatory transepithelial H+ flux regulates a rhythmic behavior in C. elegans. Curr. Biol. 18: 297-302.

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Rajendran VM., Nanda Kumar NS., Tse CM. and Binder HJ. (2015). Na-H Exchanger Isoform-2 (NHE2) Mediates Butyrate-dependent Na+ Absorption in Dextran Sulfate Sodium (DSS)-induced Colitis. J Biol Chem. 290(42):25487-96.

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Sangan, P., V.M. Rajendran, J.P. Geibel, and H.J. Binder. (2002). Cloning and expression of a chloride-dependent Na+-H+ exchanger. J. Biol. Chem. 277: 9668-9675.

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Simonin A. and Fuster D. (2010). Nedd4-1 and beta-arrestin-1 are key regulators of Na+/H+ exchanger 1 ubiquitylation, endocytosis, and function. J Biol Chem. 285(49):38293-303.

Siyanov, V. and J.M. Baltz. (2013). NHE1 is the sodium-hydrogen exchanger active in acute intracellular pH regulation in preimplantation mouse embryos. Biol Reprod 88: 157.

Slepkov, E.R., S. Chow, M.J. Lemieux, and L. Fliegel. (2004). Proline residues in transmembrane segment IV are critical for activity, expression and targeting of the Na+/H+ exchanger isoform 1. Biochem. J. 379: 31-38.

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Tse, C.M., A.I. Ma, V.W. Yang, A.J. Watson, S. Levine, M.H. Montrose, J. Potter, C.Sardet, J. Pouysségur, and M. Donowitz. (1991). Molecular cloning and expression of a cDNA encoding the rabbit ileal villus cell basolateral membrane Na+/H+ exchanger. EMBO J. 10: 1957-1967.

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Ullah A., Kemp G., Lee B., Alves C., Young H., Sykes BD. and Fliegel L. (2013). Structural and functional analysis of transmembrane segment IV of the salt tolerance protein Sod2. J Biol Chem. 288(34):24609-24.

Uzdavinys, P., M. Coinçon, E. Nji, M. Ndi, I. Winkelmann, C. von Ballmoos, and D. Drew. (2017). Dissecting the proton transport pathway in electrogenic Na/H antiporters. Proc. Natl. Acad. Sci. USA 114: E1101-E1110.

Venema, K., F.J. Quintero, J.M. Pardo, and J.P. Donaire. (2002). The Arabidopsis Na+/H+ exchanger AtNHX1 catalyzes low affinity Na+ and K+ transport in reconstituted liposomes. J. Biol. Chem. 277: 2413-2418.

Verkhovskaya, M.L., B. Barquera, and M. Wikström. (2001). Deletion of one of two Escherichia coli genes encoding putative Na+/H+ exchangers (ycgO) perturbs cytoplasmic alkali cation balance at low osmolarity. Microbiology 147: 3005-3013.

Verma, D., S.L. Singla-Pareek, D. Rajagopal, M.K. Reddy, and S.K. Sopory. (2007). Functional validation of a novel isoform of Na+/H+ antiporter from Pennisetum glaucum for enhancing salinity tolerance in rice. J Biosci 32: 621-628.

Waditee, R., T. Hibino, T. Nakamura, A. Incharoensakdi, and T. Takabe. (2002). Overexpression of a Na+/H+ antiporter confers salt tolerance on a freshwater cyanobacterium, making it capable of growth in sea water. Proc. Natl. Acad. Sci. USA 99: 4109-4114.

Waditee, R., T. Hibino, Y. Tanaka, T. Nakamura, A. Incharoensakdi, and T. Takabe. (2001). Halotolerant cyanobacterium Aphanothece halophytica contains an Na+/H+ antiporter, homologous to eukaryotic ones, with novel ion specificity affected by C-terminal tail. J. Biol. Chem. 276: 36931-36938.

Wakabayashi, S., T. Hisamitsu, and T.Y. Nakamura. (2013). Regulation of the cardiac Na+/H+ exchanger in health and disease. J Mol. Cell Cardiol 61: 68-76.

Wakabayashi, S., T. Pang, X. Su, and M. Shigekawa. (2000). A novel topology model of the human Na+/H+ exchanger isoform 1. J. Biol. Chem. 275: 7942-7949.

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Wang, X., F. Xu, and S. Chen. (2013). Metagenomic cloning and characterization of Na⁺/H⁺ antiporter genes taken from sediments in Chaerhan Salt Lake in China. Biotechnol Lett 35: 619-624.

Wang, X., R. Yang, B. Wang, G. Liu, C. Yang, and Y. Cheng. (2011). Functional characterization of a plasma membrane Na+/H+ antiporter from alkali grass (Puccinellia tenuiflora). Mol Biol Rep 38: 4813-4822.

Wang, Y., C. Pan, Q. Chen, Q. Xie, Y. Gao, L. He, Y. Li, Y. Dong, X. Jiang, and Y. Zhao. (2023). Architecture and autoinhibitory mechanism of the plasma membrane Na/H antiporter SOS1 in Arabidopsis. Nat Commun 14: 4487.

Wei, Y., J. Liu, Y. Ma, and T.A. Krulwich. (2007). Three putative cation/proton antiporters from the soda lake alkaliphile Alkalimonas amylolytica N10 complement an alkali-sensitive Escherichia coli mutant. Microbiology. 153: 2168-2179.

Wells, K.M. and R. Rao. (2001). The yeast Na+/H+ exchanger Nhx1 is an N-linked glycoprotein. J. Biol. Chem. 276: 3401-3407.

Wen, J., S. Chen, M. Bao, C. Hu, L. Wu, Y. Yong, X. Liu, Y. Li, Z. Yu, X. Ma, J.B. Eun, J.H. Shim, M. Warda, A.M. Abd El-Aty, and X. Ju. (2023). Slc9a1 plays a vital role in chitosan oligosaccharide transport across the intestinal mucosa of mice. Carbohydr Polym 299: 120179.

Wiebe, S.A., A. Plain, W. Pan, D. O''Neill, B. Braam, and R.T. Alexander. (2019). NHE8 attenuates calcium influx into NRK cells and the proximal tubule epithelium. Am. J. Physiol. Renal Physiol. [Epub: Ahead of Print]

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Xiang, M., M. Feng, S. Muend, and R. Rao. (2007). A human Na+/H+ antiporter sharing evolutionary origins with bacterial NhaA may be a candidate gene for essential hypertension. Proc. Natl. Acad. Sci. U.S.A. 104: 18677-186781.

Yan, J.J., M.Y. Chou, T. Kaneko, and P.P. Hwang. (2007). Gene expression of Na+/H+ exchanger in zebrafish H+-ATPase-rich cells during acclimation to low-Na+ and acidic environments. Am. J. Physiol. Cell Physiol. 293: C1814-1823.

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Yang, L.F., J.Q. Jiang, B.S. Zhao, B. Zhang, d.e.Q. Feng, W.D. Lu, L. Wang, and S.S. Yang. (2006). A Na+/H+ antiporter gene of the moderately halophilic bacterium Halobacillus dabanensis D-8T: cloning and molecular characterization. FEMS Microbiol. Lett. 255: 89-95.

Yin, Y.L., H.H. Wang, Z.C. Gui, S. Mi, S. Guo, Y. Wang, Q.Q. Wang, R.Z. Yue, L.B. Lin, J.X. Fan, X. Zhang, B.Y. Mao, T.H. Liu, G.R. Wan, H.Q. Zhan, M.L. Zhu, L.H. Jiang, and P. Li. (2022). Citronellal Attenuates Oxidative Stress-Induced Mitochondrial Damage through TRPM2/NHE1 Pathway and Effectively Inhibits Endothelial Dysfunction in Type 2 Diabetes Mellitus. Antioxidants (Basel) 11:.

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Zhang, W., W. Fan, J. Guo, and X. Wang. (2022). Osmotic stress activates RIPK3/MLKL-mediated necroptosis by increasing cytosolic pH through a plasma membrane Na/H exchanger. Sci Signal 15: eabn5881.

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Zörb, C., A. Noll, S. Karl, K. Leib, F. Yan, and S. Schubert. (2005). Molecular characterization of Na+/H+ antiporters (ZmNHX) of maize (Zea mays L.) and their expression under salt stress. J Plant Physiol. 162: 55-66.

Zou, Y.J., L.F. Yang, L. Wang, and S.S. Yang. (2008). Cloning and characterization of a Na+/H+ antiporter gene of the moderately halophilic bacterium Halobacillus aidingensis AD-6T. J Microbiol 46: 415-421.


TC#NameOrganismal TypeExample

Na+:H+ antiporter 1 (Nhe-1) (Regulated by Daxx (O35613)). An integral membrane protein that regulates intracellular pH and has a large N-terminal membrane domain of 12 transmembrane segments and an intracellular C-terminal regulatory domain (Reddy et al., 2008). The dimer catalyzes antiport with 2Na+/2H+ stoichiometry (Fuster et al., 2008). Nedd4-1 and β-arrestin-1 are key regulators of Na+/H+ exchanger 1 ubiquitylation, endocytosis and function (Simonin and Fuster et al., 2010). Important in heart disease and cancer. Structural studies have been performed using NMR (Lee et al., 2011). Analyses of heart disease and the involvement of cell regulatory systems have been proposed (Li et al. 2023).


Nhe-1 of Rattus norvegicus

2.A.36.1.10Basal membrane Nhe3 AnimalsNhe3 of Aedes aegypti (Q17L17)

The Na+:H+ Exchanger, NHE1, is developmentally regulated and necessary for cell polarity (Patel and Barber, 2005).

Slime Molds

NHE1 of Dictyostelium discoideum (Q552S0)


Na+:H+ antiporter, NHX1; (vacuolar/endosomal Na+ tolerance protein).  Plays roles in ion homeostasis and vesicle trafficing (Mukherjee et al. 2006). The structures and functions of these NHX homologues have been reviewed (Dutta and Fliegel 2018). K+ influx/efflux regulates mitochondrial energetics while maintaining mitochondrial ionic balance and volume homeostasis (Malas et al. 2022).

Yeast; plants

NHX1 (YDR456w) of Saccharomyces cerevisiae


Na+ /H+ exchanger-1 (NHE1).  Stoichiometry = 1:1. TMS VI of NHE1 is a discontinuous pore-lining helix with residues Asn(227), Ile(233), and Leu(243) lining the translocation pore (Tzeng et al., 2010). (orthologous to NHE1 of rat, TC# 2.A.36.1.1). Both Pro167 and Pro168 in TMS IV are required for normal NHE activity (Slepkov et al. 2004). NHE1 regulates internal pH in human monocytes and is important in heart disease and cancer (Tsai et al. 2015). Structural studies have been performed using NMR and EPR (Lee et al., 2011; Nygaard et al. 2011).  Extracytoplasmic loops contribute to ion coordination and inhibitor sensitivity (Lee et al. 2012).  The regulation of NHE1 has been reviewed (Wakabayashi et al. 2013).  CD44 (LHR, MDU2, MDU3, MIC4; P16070; TC# 9.B.87.1.31) regulates breast cancer metastasis by regulating NHE1 expression (Chang et al. 2014).  The role of NHE1 in kidney proximal tubule functions, including pH regulation, vectorial Na+ transport, cell volume control and cell survival has been reviewed (Parker et al. 2015).  Helix M9 and the adjacent exofacial re-entrant loop 5 between M9 and M10 (EL5) are important elements involved in cation transport and inhibitor sensitivity (Jinadasa et al. 2015).  A 12 TMS topology has been confirmed (Liu et al. 2015).  Mutations  cause Lichtenstein-Knorr syndrome, an autosomal recessive condition that associates sensorineural hearing loss with cerebellar ataxia (Guissart et al. 2015). Cleaved FAS ligand (transmembrane CD95L; 1 TMS; P48023) activates NHE1 through the Akt/ROCK1 signalling pathway to stimulate cell motility (Monet et al. 2016). NHE1 may contribute to internal pH and motility of mammalian sperm (Muzzachi et al. 2018). NHE1 appears to be the only significant regulator of intracellular pH in preimplantation mouse embryos (Siyanov and Baltz 2013). The intracellular loop, IL5, is critical for proton sensing and ion transport (Wong et al. 2018). NHE1 and CD44 (the hyaluronan receptor with 742 aas and 2 TMSs, one at the N-terminus and one at the C-terminus (P16070)) appear to play important roles in cardiac remodeling (Suleiman et al. 2018). A three-dimensional model of NHE1, accounting for inhibitor binding, has been proposed (Dutta and Fliegel 2019). It forms a complex with Kv11.1 (TC# 1.A.1.20.1) and β-integrin (TC# 9.B.87.1.25). Activation of Na+/H+ exchanger isoform 1 is regulated by the extracellular environment and protein cofactors, including calcineurin B homologous proteins 1 and 2 (Cottle et al. 2020). NHE1, a central regulator of transmembrane pH that supports carcinogenic progression, is inhibited by 5- and 6-substituted amilorides (Buckley et al. 2021). The roles of NHE1 in health and disease have been reviewed (Fliegel 2021). Citronellal suppresses the expression of NHE1 and TPRM2, alleviates oxidative stress-induced mitochondrial damage, and imposes a protective effect on endothelial dysfunction in type 2 diabetes mellitus rats (Yin et al. 2022). Osmotic stress increases the intracellular pH through SLC9A1 (Zhang et al. 2022). Oxaliplatin (OHP)-induced intracellular acidification of dorsal root ganglion (DRG) neurons largely depends on calcineurin (CaN)-mediated NHE1 inhibition, revealing new mechanisms that OHP can exert to alter neuronal excitability (Dionisi et al. 2023). Slc9a1 plays a vital role in chitosan oligosaccharide transport across the intestinal mucosa of mice (Wen et al. 2023).


SLC9A1 of Homo sapiens


Sodium/hydrogen exchanger 6 (Na+/H+ exchanger 6) (NHE-6) (Solute carrier family 9 member 6; SLC9A6).  This Na+/H+ exchanger is encoded by an X-linked gene that is widely expressed and especially abundant in brain, heart and skeletal muscle where it is implicated in endosomal pH homeostasis and trafficking as well as maintenance of cell polarity. Several mutations in the coding region of NHE6 are linked with severe intellectual disability, autistic behavior, ataxia and other abnormalities (Ilie et al. 2014).  A Christianson syndrome-linked mutation disrupts endosomal function and elicits neurodegeneration and cell death (Ilie et al. 2016; Hussain et al. 2023.  Heterozygous female mice suffer from visuospatial memory and motor coordination deficits similar to but less severe than those observed in X-chromosome hemizygous mutant males (Sikora et al. 2016).


SLC9A6 of Homo sapiens


Sodium/hydrogen exchanger 3 (Na+/H+ exchanger 3) (NHE-3) of 834 aas and 12 TMSs (Solute carrier family 9 member 3) (Dominguez Rieg et al. 2016). SLC9A3 deficiency-mediated micturition dysfunction is caused by electrolyte imbalance (Chen et al. 2023).


SLC9A3 of Homo sapiens

2.A.36.1.16Sodium/hydrogen exchanger 5 (Na(+)/H(+) exchanger 5) (NHE-5) (Solute carrier family 9 member 5)AnimalsSLC9A5 of Homo sapiens

Sodium/hydrogen exchanger 2 (Na+/H+ exchanger 2) (NHE-2 or NHE2) (Solute carrier family 9 member 2).  Mediates butyrate-dependent Na+ absorption (Rajendran et al. 2015).


SLC9A2 of Homo sapiens

2.A.36.1.18Sodium/hydrogen exchanger 4 (Na(+)/H(+) exchanger 4) (NHE-4) (Solute carrier family 9 member 4)AnimalsSLC9A4 of Homo sapiens

Sodium/hydrogen exchanger 9 (Na+/H+ exchanger 9) (NHE-9; NHE9) (Solute carrier family 9 member 9, SLC9A9) of 645 aas and 12 TMSs. It may act in electroneutral exchange of protons for Na+ across membranes and is involved in the effusion of Golgi luminal H+ in exchange for cytosolic cations. It is also involved in organellar ion homeostasis by contributing to the maintenance of the unique acidic pH values of the Golgi and post-Golgi compartments in the cell (Nakamura et al. 2005). The cryogenic electron microscopy structure of NHE9 from Equus caballus at 3.2 A resolution has been determined (Winklemann et al. 2020). It is an endosomal isoform highly expressed in the brain and associated with autism spectrum (ASD) and attention deficit hyperactivity (ADHD) disorders in humans. The NHE9 architecture and ion-binding site are similar to distantly related bacterial Na+/H+ antiporters with 13 transmembrane segments. The conserved architecture of the NHE ion-binding site, their elevator-like structural transitions, the functional implications of autism disease mutations and the role of phosphoinositide lipids to promote homodimerization that, together, have important physiological ramifications have been revealed (Winklemann et al. 2020).



SLC9A9 of Homo sapiens


Na+:H+ antiporter 3 (NHE-3 or NHE3). Regulated by Na+/H+ exchange regulatory cofactors (NHERF; O14745; TC #8.A.24.1.1) (Seidler et al., 2009). Cyclic AMP-mediated endocytosis of intestinal epithelial NHE3 requires binding to synaptotagmin 1 (Musch et al., 2010).  Decreased activity is responsible for congenital Na+ diarrhea in the human brush boarder (Janecke et al. 2015). Reduced functional expression of NHE3, and DRA contribute to Cl- and Na+ stool loss in microvillus inclusion disease (MVID) diarrhea (Kravtsov et al. 2016).


Nhe-3 of Rattus norvegicus


Endomembrane (Golgi) K+, Na+/H+ exchanger 5, NHX5, of 521 aas and 11 TMSs.  Three acidic residues are critical for transport activity as well as seedling growth, regulation of protein transport into vesicles and ionic homeostasis (Qiu 2016). NHX6 is 80% identical to NHX5 (535 aas and 11 TMSs) and serves the same function. They are all located in Golgi, trans-Golgi network (TGN), endoplasmic reticulum (ER) and prevacuolar compartment (PVC). They are critical for salt tolerance stress and the homeostasis of pH and K+ (Wang 2019).


NHX5 of Arabidopsis thaliana (Q9SLJ7)


Na+/H+ exchanger, beta-like, NHE, of 917 aas and 11 putative TMSs.  Involved in pH homeostasis (Li et al. 2019).

NHE of Penaeus vannamei (Pacific white shrimp)


Sodium/proton exchanger of 529 aas and 12 or 13 TMSs.  The six NHXs in grape have been bioinformatically characterized (Ayadi et al. 2019). This protein is 81% identical to the exchanger with TC# 2.A.36.1.5.

NHX6 of Vitis vinifera (wine grape)


Sodium/hydrogen exchanger 2a NHE2a, of 818 aas and 13 TMSs.  Expression of several NHE genes were regulated bylow, isotonic or high salinity treatments, indicating an involvements in salinity and osmotic regulation in teleosts (Liu et al. 2019).

NHE2a of Lateolabrax maculatus


Na+/K+:H+ antiporter, Nhe-7, present in the Golgi apparatus and endosomes. There are four isoforms, NHE6-9. They regulate the luminal pH as well as intracellular trafficking, and function in cell polarity development (Ohgaki et al., 2011). Nhe-6 (Nhe6) is associated with X-linked intellectural disability and autism when processing and trafficking is impaired (Ilie et al. 2013).


SLC9A7 of Homo sapiens

2.A.36.1.4Cl--dependent Na+:H+ antiporter (Nhe) (residues 1-375 are identical to Nhe-1 [TC #2.A.36.1.1]).AnimalsNhe of Rattus norvegicus
2.A.36.1.5Na+/K+:H+ antiporter, NHX2PlantsNHX2 of Lycopersicon esculentum (CAC83608)
2.A.36.1.6Zebrafish Na+:H+ antiporter NheC (Yan et al., 2007) (most similar to TC# 2.A.36.1.2, 48% identical)AnimalsNheC of Danio rerio (A3KPJ8)
2.A.36.1.7The basolateral intestinal Na+/H+ antiporter PBO-4 (Beg et al., 2008)Animals PBO-4 of Caenorhabditis elegans (Q21386)
2.A.36.1.8Na+/H+ exchanger, Nhx-2 (Pfeiffer et al., 2008) AnimalsNhx-2 of Caenorhabditis elegans (Q09432)

Human Na+/H+ Exchanger, NHE-8 or SLC9A8. Functions in intracellular pH homeostasis, cell volume regulation, and electroneutral NaCl absorption in epithelia. It attenuates Ca2+ influx in the proximal tubular epithelium (Wiebe et al. 2019).


SLC9A8 of Homo sapiens


TC#NameOrganismal TypeExample

Putative Na+/H+ exchanger, Cpa1 (399aas; 13 TMSs)


Cpa1 of Methanothermobacter thermautotrophicus (O26854)


The electroneutral Na+/Li+:H+ antiporter, Nha2. Catalyzes Na+:Li+ antiport; contributes to salt homeostasis. It correlates with heritable hypertension (Xiang et al., 2007) and is critical for insulin secretion (Deisl et al. 2013). Like electrogenic Na+/H+ exchangers, it has two conserved aspartyl residues in the Na+ binding site but seems to be electroneutral (Uzdavinys et al. 2017). The structure, mechanism and lipid-mediated remodeling of the mammalian Na+/H+ exchanger NHA2, linked to the pathogenesis of diabetes mellitus, have been described (Matsuoka et al. 2022). NHA2 consists of 14 TMSs, rather than the 13 previously observed in mammalian NHEs and related bacterial antiporters. The additional N-terminal helix in NHA2 forms a unique homodimer interface with a large intracellular gap between the protomers, which closes in the presence of phosphoinositol lipids. Possibly the additional N-terminal helix has evolved as a lipid-mediated remodeling switch for the regulation of NHA2 activity (Matsuoka et al. 2022).



SLC9B2 of Homo sapiens

2.A.36.2.3 solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1AnimalsSLC9B1 of Homo sapiens

TC#NameOrganismal TypeExample

Putative antiporter of 549 aas (function unknown) (Verkhovskaya et al. 2001).


YjcE of E. coli

2.A.36.3.2Na+, K+, Li+, Rb+:H+ antiporter, YvgPBacteriaYvgP of Bacillus subtilis (CAB15347)
2.A.36.3.3Uncharacterized Na(+)/H(+) exchanger Rv2287/MT2345BacteriaRv2287 of Mycobacterium tuberculosis

TC#NameOrganismal TypeExample

[Na+ or K+]:H+ antiporter Nha1 of 985 aas and 13 or 14 predicted TMSs, all at the N-terminus of the protein in a possible 6 +1 + 6 TMS arrangement. The ceontral TMS is much lower in hydrophobicity than the other TMSs.  All TMSs are in residues 1 - 430 while the rest of the protein is strongly hydrophilic.


Nha1 (YLR138w) of Saccharomyces cerevisiae


Na+:H+ antiporter, Nha2 or Sod2-22.  Exports Na+ and Li+ but not K+.  Three residues, T141 in TMS 4, A179 in TMS 5 and V375 in TMS 11, determine the cation selectivity (Kinclova-Zimmermannova et al. 2015).


Nha2 of Zygosaccharomyces rouxii


Na+:H+ antiporter, Nha1 or Sod2 of 468 aas and 12 or 13 TMSs.  It provides salt tolerance by removing sodium and lithium ions in exchange for protons, and TMS 4 plays an important role (Ullah et al. 2013). The Asp266/Asp267 pair are critical for Sod2 function (Fliegel 2005). Residues within TMS 11 also play important roles in transport, suggesting that this TMS forms part of the ion translocation core (Dutta et al. 2017). Conserved transmembrane charged residues and a yeast-specific extracellular loop are also important for function (Dutta et al. 2019).


Nha1 of Schizosaccharomyces pombe

2.A.36.4.4The K+, Rb+ and other alkali metal cation efflux porter, Cnh1 (Kinclova-Zimmermannova and Sychrova, 2007). Transports Na+, K+, Li+ and Rb+ in several Candida species.  Confers tolerance to high salt concentrations (Krauke and Sychrova 2008).


Cnh1 of Candida albicans (Q9P937)

2.A.36.4.5Probable Na(+)/H(+) antiporter C3A11.09YeastSPAC3A11.09 of Schizosaccharomyces pombe

TC#NameOrganismal TypeExample

Low-affinity Na+ (K+, Li+ or Cs+):H+ antiporter, Nhx1. It is up-regluated in response to high salt stress conditions (Yang et al. 2018). It has the same general architecture as CHX17 of A. thaliana (TC# 2.A.37.4.2) (Sze and Chanroj 2018). Four NHX proteins (1-4) have been identified in Argania spinosa L (Karim et al. 2020).


Nhx1 of Arabidopsis thaliana


Vacuolar Na+/H+ antiporter, NHX1. A class-I type NHX. Confers NaCl tolerance and therefore pumps Na+ from the cytosol to the vacuole (Jha et al., 2011).

Halophytic plants

NHX1 of Salicornia brachiata (B1PLB6)


Vacuolar Na+/H+ exchanger, DgNHX1 or NHX1, of 510 aas and 13 putative (but possibly 9 actual) TMSs. Involved in adaptation to salt stress conditions and expressed under these same conditions (Liu et al. 2013). 


NHX1 of Chrysanthemum morifolium (Florist's daisy) (Dendranthema grandiflorum)


Vacuorlar Na+/H+ exchanger, Nhx1 of 542 aas and 13 TMSs.  Involved in salt tolerance (Mishra et al. 2014).


Nhx1 of Vigna radiata (Mung bean)


Na+:H+ antiporter, Nhx1 of 470 aas and 9 TMSs. NHX1 can confer a high level of salinity tolerance when overexpressed in Brassica juncea. Verma et al. 2007 reported its functional characterization. Overexpression conferred a high level of salinity tolerance in rice. Transgenic rice plants overexpressing PgNHX1 developed more extensive root systems and completed their life cycle by setting flowers and seeds in the presence of 150 mM NaCl.

Nhx1 of Pennisetum americanum (Pearl millet) (Pennisetum glaucum)


Na+/Li+/H+ exchanger of 545 aas and 12 TMSs, NHX3.  It is localized to the tonoplast membrane where it increases salt tolerance and reduces Li+ toxicity.  TMS 11 is important in Li+ and Na+ transport (Pan et al. 2017).

NHX3 of Populus euphratica (Euphrates poplar)


Na+:H+ antiporter, NHX4 of 538 aas and 12 TMSs. The relationships of the expression of the six maize  NHX proteins with salt resistance of maize have been examined (Zörb et al. 2005). Upon high salt (NaCl) stress in Aelurtopus lagopoides, the amount of the probable ortholog (78% identcal) increases (Ahmed et al. 2013). This protein is of the same length and topology with 79% identity as the ortholog in Triticum aestivum which may facilitate differential abiotic stress tolerance (Sharma et al. 2020).

NHX4 of Zea mays (Maize)


Sodium/hydrogen exchanger 4, NHX4, of 529 aas and 8 TMSs. This endosomal protein is critical for salt tolerance in cotton (Ma et al. 2020). It probably acts as a low affinity electroneutral exchanger of protons for cations such as Na+ or K+ across membranes, but may also exchange Li+ and Cs+ with lower affinities.

NHX4A of Arabidopsis thaliana (Mouse-ear cress)


The sodium/hydrogen exchanger 2, NHX2, of 546 aas and 13 TMSs. It catalyzes the low affinity electroneutral exchange of protons for cations such as Na+ or K+ across membranes, and may also exchange Li+ and Cs+ with a lower affinity. It is involved in vacuolar ion compartmentalization necessary for cell volume regulation and cytoplasmic Na+ detoxification (Yokoi et al. 2002). Its ortholog has also been studied in Phyllostachys edulis (moso bamboo) where its overexpression reduces salt tolerance (Wu et al. 2021).


NHX2 of Arabidopsis thaliana (Mouse-ear cress)


TC#NameOrganismal TypeExample
2.A.36.6.1Putative Na+:H+ antiporter, Nhe2 Archaea The AF0846 gene (Nhe2) of Archaeoglobus fulgidus

Na+/H+ antiporter of 403 aas and 11 predicted TMSs, NhaH. Exchanges Na+ or Li+ but not K+ for H+ (Zou et al. 2008).  Confers Na+ and Li+ tolerance.

NhaH of Halobacillus aidingensis


Na+/H+ antiporter, NhaP2 (YcgO; CvrA) of 578 aas and 13 TMSs. Involved in growth at low osmolarity, intracellular K+ maintenance, and volume regulation (Verkhovskaya et al. 2001).

NhaP2 of E. coli


Na+ (Li+):H+ antiporter NhaG (Gouda et al. 2001).  Several very similar antiporters have been isolated from uncultured bacteria from a lake in China (Wang et al. 2013).


NhaG of Bacillus subtilis ATCC9372


K+:H+ antiporter, KhaP2 (NhaP2). Participates in volume control under low osmorality conditions (Radchenko et al., 2006; Resch et al., 2010)


KhaP2 of Vibrio parahaemolyticus (Q87KV8)

2.A.36.6.4The K+(NH4+):H+ antiporter, NhaP (confers alkali resistance for alkaline pH homeostasis) (Wei et al., 2007)BacteriaNhaP of Alkalimonas amylolytica (Q0ZAH6)

K+:H+ antiporter NhaP2 (catalyzes K+:H+ and Na+:H+ exchange; Resch et al., 2010). (84% identical to 2.A.36.6.3). A cation binding pocket in the middle of the membrane and a pathway leading to it have been identified (Mourin et al. 2018). There are 3 NhaP types in Vibrio cholerae (Vc-NhaP1, 2, and 3).  They are critical for maintenance of K+ homeostasis in the cytoplasm, and all 3 are required for cell survival at low pHs, suggesting a role in acid tolerance (Mourin et al. 2019). The solution structure of the N-terminal cytoplasmic domain of ~200 aas has been solved (Orriss et al. 2020). It reveals a compact N-terminal domain which resembles a Regulator of Conductance of K+ channels (RCK) domain connected to a more open C-terminal domain via a flexible 20 amino acid linker. NMR titration experiments showed that the protein binds ATP through its N-terminal domain (Orriss et al. 2020). Modified amiloride analogs with promising binding properties have been developed. Four selected drugs interacted with functionally important amino acid residues located on the cytoplasmic side of TMS VI, the extended chain region of TMSs V and XII, and the loop region between TMSs VIIII and IX (Mourin et al. 2021).


NhaP2 of Vibrio cholerae (Q9KNM9)


Na+/H+ antiporter 1 (MjNhaP1).  NhaP1 is a dimer with 13 TMSs per monomer as revealed by electron crystalography of 2-d crystals (Goswami et al. 2011).  This structure is contrasted with that of the distantly related bacterial NhaA; these two structures are quite different in detail, but similar within the 6 TMS repeat unit. Asp234/235 of helix VIII are involved in ligand-binding, and helix X plays a role in the activation of the transporter (Kedrov et al. 2007).


MJ0057 (NhaP1) of Methanocaldococcus jannaschii


NhaH Na+/Li+/H+ antiporter (Yang et al. 2006).


NhaH of Halobacillus dabanensis (Q2XWL3)


Na+/H+ antiporter of 424 aas, NhaP, that extrudes sodium in exchange for external protons. Has weak (if any) Li+/H+ antiport activity (Kuroda et al. 2004).

NhaP of Pseudomonas aeruginosa


Na+/H+ antiporter, NhaP, of 443 aas.  Several 3-d structures are known (Wöhlert et al. 2014).  The ion is coordinated by three acidic side chains, a water molecule, a serine and a main-chain carbonyl in an unwound stretch of TMS 5 at the deepest point of a negatively charged cytoplasmic funnel. A second narrow polar channel may facilitate proton uptake from the cytoplasm. Transport activity is cooperative at pH 6 but not at pH 5, due to pH-dependent allosteric coupling of protomers through two histidines at the dimer interface (Wöhlert et al. 2014).

NhaP of Pyrococcus abyssi


TC#NameOrganismal TypeExample

ApNhaP: a Na+:H+ antiporter at pH 5-9; a Ca2+:H+ antiporter at alkaline pH (not an Li:H+ antiporter) (Waditee et al. 2001).  When the gene for ApNhaP is expressed in the fresh water cyanobacterium, Synechococcus sp. PCC 7942, it became salt tolerant and could live in salt water (Waditee et al. 2002; ).


ApNhaP of Aphanothece halophytica


Na+/H+ antiporter of 1145 aas and 12 TMSs, SOS1.  Suppresses salt (200 mM NaCl) sensitivity, promoting tolerance (Wu et al. 2007). It is 65% identical to the A. thaliana homologue (TC# 2.A.36.7.6). In Solanum tuberosum, there are 37 salt overly sensitive 1 (SOS1) genes (Liang et al. 2023). Most of the gene products are located in the plasma membrane. Promoter analysis revealed that the majority of these StSOS1 genes contain abundant cis-elements involved in various abiotic stress responses. Tissue specific expression showed that 21 of the 37 StSOS1s are widely expressed in various tissues or organs of the potato. Molecular interaction network analysis suggests that 25 StSOS1s may interact with other proteins involved in potassium ion transmembrane transport and response to salt stress. RT-qPCR results revealed that the expression of StSOS1s are significant modulated by various abiotic stresses, in particular salt and abscisic acid stress (Liang et al. 2023). 

SOS1 of Populus euphratica (Euphrates poplar)

2.A.36.7.2Low affinity (Km=8 mM) Na+(Li+):H+ antiporter, NhaS1BacteriaNhaS1 of Synechocystis sp. PCC6803

Li+/H+ antiporter, AtNHX8 (An et al., 2007).  An orthologue in Puccinellia tenuiflora (alkali grass) is up regulated under salt stress and confers tolerance to high NaCl stress (Wang et al. 2011).  SlNHX6 and SlNHX8 from tomato, are significantly upregulated by salt shock in open flower tissues (Cavusoglu et al. 2023).


NHX8 of Arabidopsis thaliana (Q3YL57)

2.A.36.7.4Sodium/hydrogen exchanger 11 (Na(+)/H(+) exchanger 11) (NHE-11) (Solute carrier family 9 member 11) (Solute carrier family 9 member C2)AnimalsSLC9C2 of Homo sapiens

Sodium/hydrogen exchanger 10 (Na+/H+ exchanger 10) (NHE-10) (Solute carrier family 9 member 10) (Solute carrier family 9 member C1) (Sperm-specific Na+/H+ exchanger) (sNHE).  It is predicted to have 17 TMSs in a 13 +  4 TMS arrangement.  The last 4 TMSs are homologous to the 4 TMS voltage sensor of the Ca2+ channel, 1.A.1.11.7. sNHE is a target for inhibition, for use in male contraception, causing inhibition of sperm motility (Mariani et al. 2023). Ion currents through the voltage sensor domains (VSDs) of distinct families of proteins have been studied (Arcos-Hernández and Nishigaki 2023).  The VSD confers voltage sensitivity to different types of transmembrane proteins such as (1) voltage-gated ion channels, (2) the voltage-sensing phosphatase (Ci-VSP), and (3) this sperm-specific Na+/H+ exchanger (sNHE). VSDs contain four TMSs (S1-S4) and several positively charged amino acids in S4, which are essential for the voltage sensitivity of the protein. Generally, in response to changes in the Vm, the positive residues of S4 displace along the plasma membrane without generating ionic currents through this domain. However, some native (e.g., Hv1 channels) and mutants of VSDs produce ionic currents. These gating pore currents are usually observed in VSDs that lack one or more of the conserved positively charged amino acids in S4. The gating pore currents can also be induced by the isolation of a VSD from the rest of the protein domains. Arcos-Hernández and Nishigaki 2023 summarized gating pore currents from all families of proteins with VSDs with classification into three cases: (1) pathological, (2) physiological, and (3) artificial currents.  SLC9C1, underlies hyperpolarization and cyclic nucleotide stimulated proton fluxes across sperm membranes and regulates their hyperactivated motility. It is the first known instance of an ion transporter that uses a canonical voltage-sensing domain (VSD) and an evolutionarily conserved cyclic nucleotide binding domain (CNBD) to influence the dynamics of its ion-exchange domain (ED) (Chowdhury and Pal 2023).  Binding of cAMP causes large conformational changes in the cytoplasmic domains and disrupts key ARD-linked interfaces. These structural changes rescue the transmembrane domains from an auto-inhibited state and facilitate their functional dynamics (Chowdhury and Pal 2023).


SLC9C1 of Homo sapiens


Dimeric Salt-Overly-Sensitive 1 (SOS1) sodium:proton exchanger 7 (NHX7) (Núñez-Ramírez et al. 2012).  The salt stress-induced SOS pathway in A. thaliana involves the perception of a calcium signal by the SOS3 and SOS3-like CALCIUM-BINDING PROTEIN8 (SCaBP8; TC# 5.B.1.1.8) calcium sensors, which then interact with and activate the SOS2 protein kinase (9.B.106.3.4), forming a complex at the plasma membrane that activates the SOS1 Na⁺/H⁺ exchanger (Lin et al. 2014).  The involvement of SOS1 in Na+ efflux in plant roots has been reviewed (Britto and Kronzucker 2015). SOS1 appears to encode a salinity-inducible plasma membrane Na+ /H+ antiporter (Song et al. 2012). ZmSWEET1b is responsible for assimilation and salt stress response in maize. It is generally important for maize plant development and responses to salt stress (Wu et al. 2023). SOS1) is an electroneutral Na+/H+ antiporter at the plasma membrane of higher plants and plays a central role in resisting salt stress. SOS1 is kept in a resting state with basal activity and activated upon phosphorylation. Wang et al. 2023 reported structures of SOS1 which forms a homodimer, with each monomer composed of transmembrane and intracellular domains. SOS1 is locked in an occluded state by shifting of the lateral-gate TM5b toward the dimerization domain, thus shielding the Na+/H+ binding site. Ddimerization of the intracellular domain stabilizes the transporter in this conformation. Moreover, two discrete fragments and a residue W1013 are important to prevent the transition of SOS1 to an alternative conformational state. A study enhances an understanding of the alternate access model of eukaryotic Na+/H+ exchangers (Wang et al. 2023).  The structure and activation mechanism of the rice SOS1 Na+/H+ antiporter has been described (Zhang et al. 2023).



SOS1 of Arabidopsis thaliana


Testis-specific sodium:proton exchanger, mtsNHE (Slc9c1) of 1175 aas and 12 - 16 TMSs.  It is present in sperm flagellae and seems to be required for optimal sperm motility, fertilization and the acrosome reaction (Liu et al. 2010).  69% identical to the human NHE, TC# 2.A.36.7.5.  It may have a 12 TMS topology, but has a long C-terminal hydrophilic domain with a segment showing 2 - 4 TMSs. 


mtsNHE of Mus musculus


Putative Na+/H+ antiporter of 1142 aas


Nha of Eimeria tenella (Coccidian parasite)


Sodium/proton antiporter, Nhe1 of 1690 aas


Nhe1 of Plasmodium falciparum


TC#NameOrganismal TypeExample