2.A.37 The Monovalent Cation:Proton Antiporter-2 (CPA2) Family

The CPA2 family is a moderately large from bacteria, archaea and eukaryotes. Among the functionally well-characterized members of the family are (1) the KefB/KefC K+ efflux proteins of E. coli which may be capable of catalyzing both K+/H+ antiport and K+ uniport, depending on conditions (Bakker et al., 1987; Booth et al., 1996; Munro et al., 1991), (2) the Na+/H+ antiporter of Enterococcus hirae (Waser et al., 1992) and (3) the K+/H+ antiporter of S. cerevisiae. It has been proposed that under normal physiological conditions, these proteins may function by essentially the same mechanism (Reizer et al., 1992).

KefC and KefB of E. coli are responsible for glutathione-gated K+ efflux (Ferguson et al., 1993, 1997). Each of these proteins consists of a transmembrane hydrophobic N-terminal domain, and a less well-conserved C-terminal hydrophilic domain. Each protein interacts with a second protein encoded by genes that overlap the gene encoding the primary transporter. The KefC ancillary protein is YabF while the KefB ancillary protein is YheR. These ancillary proteins stimulate transport activity about 10-fold (Miller et al., 2000). These proteins are important for cell survival during exposure to toxic metabolites, possibly because they can release K+, allowing H+ uptake. Activation of the KefB or KefC K+ efflux system only occurs in the presence of glutathione and a reactive electrophile such as methylglyoxal or N-ethylmaleimide. Formation of the methylglyoxal-glutathione conjugate, S-lactoylglutathione, is catalyzed by glyoxalase I, and S-lactoylglutathione activates KefB and KefC (MacLean et al., 1998). H+ uptake (acidification of the cytoplasm) accompanying or following K+ efflux may serve as a further protective mechanism against electrophile toxicity (Booth et al., 1996; Ferguson et al., 1993, 1997; Stumpe et al., 1996). Inhibition of transport by glutathione was enhanced by NADH (Fujisawa et al., 2007).

Gram negative bacteria are protected against toxic electrophilic compounds by glutathione-gated potassium efflux systems (Kef) that modulate cytoplasmic pH. Roosild et al. (2010) have elucidated the mechanism of gating through structural and functional analysis of the E. coli KefC. The revealed mechanism can explain how subtle chemical differences in glutathione derivatives can produce opposite effects on channel function. Kef channels are regulated by potassium transport and NAD-binding (KTN) domains that sense both reduced glutathione, which inhibits Kef activity, and glutathione adducts that form during electrophile detoxification and activate Kef. Roosild et al. (2010) found that reduced glutathione stabilizes an interdomain association between two KTN folds, whereas large adducts sterically disrupt this interaction. F441 is identified as the pivotal residue discriminating between reduced glutathione and its conjugates. They demonstrated a major structural change on the binding of an activating ligand to a KTN-domain protein.

The MagA protein of Magnetospirillum sp. strain AMB-1 has been reported to be required for synthesis of bacterial magnetic particles. The magA gene is subject to transcriptional activation by an iron deficiency (Nakamura et al., 1995).  However, are more recent report has shown that magA mutants of both Magnetospirillum magneticum AMB-1 and M. gryphiswaldense MSR-1 formed wild-type-like magnetosomes without a growth defect (Uebe et al. 2012). Its transport function is not known. The GerN and GrmA proteins of Bacillus cereus and Bacillus megaterium, respectively, are spore germination proteins that can exchange Na+ for H+ and/or K+ (Southworth et al., 2001). The AmhT homologue of Bacillus pseudofirmus transports both K+ and NH4+, influences ammonium homeostasis, and is required for normal sporulation and germination. The identification of these proteins as members of the CPA2 family reveals that monovalent cation transport is required for Bacillus spore formation and germination (Tani et al., 1996).

The proteins of the CPA2 family consist of between 333 and 900 amino acyl residues. They exhibit 10-14 transmembrane α-helical spanners (TMSs). Several organisms possess multiple CPA2 paralogues. Thus, E. coli has three, Methanococcus jannaschii has four and Synechocystis sp. has five paralogues. The potassium efflux system, Kef, protects bacteria against the detrimental effects of electrophilic compounds via acidification of the cytoplasm. Kef is inhibited by glutathione (GSH) but activated by glutathione-S-conjugates (GS-X) formed in the presence of electrophiles. GSH and GS-X bind to overlapping sites on Kef, which are located in a cytosolic regulatory domain (Healy et al. 2014).

Interestingly, this family proliferated in plants such as Araidopsis thaliana where there are 28 members that may function in pollen development, germination, and tube growth (Sze et al. 2004), but they are rarely found in metazoans (Bock et al. 2006). These plant proteins probably arose from their bacterial homologues (Chanroj et al. 2012) and privide functions such as osmotic adjustment and K+ homeostasis during pollen development (Sze et al. 2004). These family members show very similar 3-D folds to CPA1 family members, and this structure is called the NhaA-fold (Czerny et al. 2016). H+ pumps, counter-ion fluxes, and cation/H+ antiporters, including CPA2 family members, are probably interlinked with signaling and membrane trafficking to remodel membranes and cell walls (Sze and Chanroj 2018).


The generalized transport reaction catalyzed by members of the CPA2 family is:

M+ (in) + nH+ (out) ⇌ M+ (out) + nH+ (in).

(The carrier-mediated mode)

Some members may also catalyze:

M+ (in) ⇌ M+ (out).

(The channel-mediated mode)

This family belongs to the CPA Superfamily.



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Chanroj, S., Y. Lu, S. Padmanaban, K. Nanatani, N. Uozumi, R. Rao, and H. Sze. (2011). Plant-specific cation/H+ exchanger 17 and its homologs are endomembrane K+ transporters with roles in protein sorting. J. Biol. Chem. 286: 33931-33941.

Chen, P., X. Hao, W. Li, X. Zhao, and Y. Huang. (2016). Mutations in the TMCO3 Gene are Associated with Cornea Guttata and Anterior Polar Cataract. Sci Rep 6: 31021.

Czerny, D.D., S. Padmanaban, A. Anishkin, K. Venema, Z. Riaz, and H. Sze. (2016). Protein architecture and core residues in unwound α-helices provide insights to the transport function of plant AtCHX17. Biochim. Biophys. Acta. 1858: 1983-1998.

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Ferguson, G.P., A.W. Munro, R.M. Douglas, D. McLaggan, and I.R. Booth. (1993). Activation of potassium channels during metabolite detoxification in Escherichia coli. Mol. Microbiol. 9: 1297-1303.

Ferguson, G.P., S. Tötemeyer, M.J. MacLean, and I.R. Booth. (1998). Methylglyoxal production in bacteria: suicide or survival? Arch. Microbiol. 170: 209-219.

Ferguson, G.P., Y. Nikolaev, D. McLaggan, M. MacLean, and I.R. Booth. (1997). Survival during exposure to the electrophilic reagent N-ethylmaleimide in Escherichia coli: role of KefB and KefC potassium channels. J. Bacteriol. 179: 1007-1012.

Fujisawa, M., M. Ito, and T.A. Krulwich. (2007). Three two-component transporters with channel-like properties have monovalent cation/proton antiport activity. Proc. Natl. Acad. Sci. USA 104: 13289-13294.

Guo, Y., C. Zhu, and Z. Tian. (2023). Overexpression of Enhances Salt Tolerance in Seedlings. Curr Issues Mol Biol 45: 9692-9708.

Healy, J., S. Ekkerman, C. Pliotas, M. Richard, W. Bartlett, S.C. Grayer, G.M. Morris, S. Miller, I.R. Booth, S.J. Conway, and T. Rasmussen. (2014). Understanding the structural requirements for activators of the Kef bacterial potassium efflux system. Biochemistry 53: 1982-1992.

Hu, X., H. Zhu, S. Feng, C. Wang, Y. Ye, and X. Xiong. (2022). Transmembrane and coiled-coil domains 3 is a diagnostic biomarker for predicting immune checkpoint blockade efficacy in hepatocellular carcinoma. Front Genet 13: 1006357.

Inaba, M., A. Sakamoto, and N. Murata. (2001). Functional expression in Escherichia coli of low-affinity and high-affinity Na+(Li+)/H+ antiporters of Synechocystis. J. Bacteriol. 183: 1376-1384.

Kunz, H.H., M. Gierth, A. Herdean, M. Satoh-Cruz, D.M. Kramer, C. Spetea, and J.I. Schroeder. (2014). Plastidial transporters KEA1, -2, and -3 are essential for chloroplast osmoregulation, integrity, and pH regulation in Arabidopsis. Proc. Natl. Acad. Sci. USA 111: 7480-7485.

Lee, C., H.J. Kang, C. von Ballmoos, S. Newstead, P. Uzdavinys, D.L. Dotson, S. Iwata, O. Beckstein, A.D. Cameron, and D. Drew. (2013). A two-domain elevator mechanism for sodium/proton antiport. Nature 501: 573-577.

MacLean, M.J., L.S. Ness, G.P. Ferguson, and I.R. Booth. (1998). The role of glyoxalase I in the detoxification of methylglyoxal and in the activation of the KefB K+ efflux system in Escherichia coli. Mol. Microbiol. 27: 563-571.

Miller, S., L.S. Ness, C.M. Wood, B.C. Fox, and I.R. Booth. (2000). Identification of an ancillary protein, YabF, required for activity of the KefC glutathione-gated potassium efflux system in Escherichia coli. J. Bacteriol. 182: 6536-6540.

Miller, S., R.M. Douglas, P. Carter, and I.R. Booth. (1997). Mutations in the glutathione-gated KefC K+ efflux system of Escherichia coli that cause constitutive activation. J. Biol. Chem. 272: 24942-24947.

Munro, A.W., G.Y. Ritchie, A.J. Lamb, R.M. Douglas, and I.R. Booth. (1991). The cloning and DNA sequence of the gene for the glutathione-regulated potassium-efflux system KefC of Escherichia coli. Mol. Microbiol. 5: 607-616.

Nakamura, C., T. Kikuchi, J.G. Burgess, and T. Matsunaga. (1995). Iron-regulated expression and membrane localization of the MagA protein in Magnetospirillum sp. strain AMB-1. J. Biochem. 118: 23-27.

Ness, L.S. and I.R. Booth. (1999). Different foci for the regulation of the activity of the KefB and KefC glutathione-gated K+ efflux systems. J. Biol. Chem. 274: 9524-9530.

Radchenko, M.V., R. Waditee, S. Oshimi, M. Fukuhara, T. Takabe, and T. Nakamura. (2006). Cloning, functional expression and primary characterization of Vibrio parahaemolyticus K+/H+ antiporter genes in Escherichia coli. Mol. Microbiol. 59: 651-663.

Ramírez, J., O. Ramírez, C. Saldaña, R. Coria, and A. Peña. (1998). A Saccharomyces cerevisiae mutant lacking a K+/H+ exchanger. J. Bacteriol. 180: 5860-5865.

Reizer, J., A. Reizer, and M.H. Saier, Jr. (1992). The putative Na+/H+ antiporter (NapA) of Enterococcus hirae is homologous to the putative K+/H+ antiporter (KefC) of Escherichia coli. FEMS Microbiol. Lett. 94: 161-164.

Roosild, T.P., S. Castronovo, J. Healy, S. Miller, C. Pliotas, T. Rasmussen, W. Bartlett, S.J. Conway, and I.R. Booth. (2010). Mechanism of ligand-gated potassium efflux in bacterial pathogens. Proc. Natl. Acad. Sci. USA 107: 19784-19789.

Saier, M.H., Jr., B.H. Eng, S. Fard, J. Garg, D.A. Haggerty, W.J. Hutchinson, D.L. Jack, E.C. Lai, H.J. Liu, D.P. Nusinew, A.M. Omar, S.S. Pao, I.T. Paulsen, J.A. Quan, M. Sliwinski, T.-T. Tseng, S. Wachi, and G.B. Young. (1999). Phylogenetic characterization of novel transport protein families revealed by genome analyses. Biochim. Biophys. Acta 1422: 1-56.

Southworth, T.W., A.A. Guffanti, A. Moir, and T.A. Krulwich. (2001). GerN, an endospore germination protein of Bacillus cereus, is an Na+/H+-K+ antiporter. J. Bacteriol. 183: 5896-5903.

Stumpe, S., A. Schlösser, M. Schleyer, and E.P. Bakker. (1996). K+ circulation across the prokaryotic cell membrane: K+-uptake systems. In Transport Processes in Eukaryotic and Prokaryotic Organisms, Vol. 2 (W.N. Konings, H.R. Kaback and J.S. Lolkema, eds.), Elsevier Press, New York, pp. 473-499.

Sze, H. and S. Chanroj. (2018). Plant Endomembrane Dynamics: Studies of K/H Antiporters Provide Insights on the Effects of pH and Ion Homeostasis. Plant Physiol. 177: 875-895.

Sze, H., S. Padmanaban, F. Cellier, D. Honys, N.H. Cheng, K.W. Bock, G. Conéjéro, X. Li, D. Twell, J.M. Ward, and K.D. Hirschi. (2004). Expression patterns of a novel AtCHX gene family highlight potential roles in osmotic adjustment and K+ homeostasis in pollen development. Plant Physiol. 136: 2532-2547.

Tani, K., T. Watanabe, H. Matsuda, M. Nasu, and M. Kondo. (1996). Cloning and sequencing of the spore germination gene of Bacillus megaterium ATCC 12872: similarities to the NaH-antiporter gene of Enterococcus hirae. Microbiol. Immunol. 40: 99-105.

Tsunekawa K., Shijuku T., Hayashimoto M., Kojima Y., Onai K., Morishita M., Ishiura M., Kuroda T., Nakamura T., Kobayashi H., Sato M., Toyooka K., Matsuoka K., Omata T. and Uozumi N. (2009). Identification and characterization of the Na+/H+ antiporter Nhas3 from the thylakoid membrane of Synechocystis sp. PCC 6803. J Biol Chem. 284(24):16513-21.

Uebe, R., V. Henn, and D. Schüler. (2012). The MagA protein of Magnetospirilla is not involved in bacterial magnetite biomineralization. J. Bacteriol. 194: 1018-1023.

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.

Waser, M., D. Hess-Bienz, K. Davies, and M. Solioz. (1992). Cloning and disruption of a putative NaH-antiporter gene of Enterococcus hirae. J. Biol. Chem. 267: 5396-5400.

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.

Wei, Y., T.W. Southworth, H. Kloster, M. Ito, A.A. Guffanti, A. Moir, and T.A. Krulwich. (2003). Mutational loss of a K+ and NH4+ transporter affects the growth and endospore formation of alkaliphilic Bacillus pseudofirmus OF4. J. Bacteriol. 185: 5133-5147.

Yang, L., Y. Jin, W. Huang, Q. Sun, F. Liu, and X. Huang. (2018). Full-length transcriptome sequences of ephemeral plant Arabidopsis pumila provides insight into gene expression dynamics during continuous salt stress. BMC Genomics 19: 717.

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TC#NameOrganismal TypeExample
2.A.37.1.1Glutathione-regulated K+ efflux protein C, KefC; regulated by ancillary protein KefF (YabF)Bacteria KefCF of E. coli
KefC (P03819)
KefF (P0A754)

CPA2 family member of 627 aas and 12 TMSs

CPA2 member of Simonsiella muelleri


Transmembrane and coiled-coil domain 3, TMCO3, of 677 aas and 13 TMSs in a 1 (N-terminus) + 4 + 2 + 2 + 4 TMS (residues 255 - 670) arrangement.  When mutated, it causes cornea guttata and anterior polar cataracts (Chen et al. 2016).  The encoding gene is expressed in the human cornea, lens capsule, and choroid-retinal pigment epithelium (Chen et al. 2016). It is a prognostic biomarker that correlates with immune infiltration in hepatocellular carcinoma (Deng et al. 2021). TMCO3 may be a biomarker for liver hepatocellular carcinoma (LIHC) prognosis and immunotherapy (Hu et al. 2022).

TMCO3 of Homo sapiens


Iron-regulated MagA protein.  Deletion mutants of magA show apparently normal magnetosomes and growth in spite of an early report to the contrary (Uebe et al. 2012).

Magnetotactic bacteria

MagA of Magnetospirillum sp. strain AMB-1


Glutathione-regulated K+ efflux protein B, KefB; regulated by ancillary protein KefG (YheR)


KefBG of E. coli
KefB (P45522)
KefG (P0A756)

2.A.37.1.3The K + efflux pump, KefB (Wei et al., 2007)BacteriaKefB of Alkalimonas amylolytica (Q0ZAH7)

K+ efflux antiporter 1, chloroplastic (AtKEA1).  It localizes to the chloroplast inner envelope membrane and is essential for normal osmoregulation (Kunz et al. 2014). It has an even number of TMSs, probably 14, with N- and C-terminal hydrophilic regulatory domains (Bölter et al. 2019). 


KEA1 of Arabidopsis thaliana


Inner membrane protein, YbaL or KefB: glutathione-regulated potassium-efflux system protein.


YbaL of Escherichia coli


K+ efflux - K+:H+ antiporter 3 (AtKEA3) of 776 aas and 13 TMSs.  Localizes to the thylakoid membrane of the chloroplast.  It modulates pmf partitioning through H+ efflux from the lumen, which is critical for photosynthetic acclimation after transitions from high to low light intensity (Armbruster et al. 2014; Kunz et al. 2014). It has an even number of TMSs, probably 14 (Bölter et al. 2019), with hydrophilic N- and C-terminal regulatory domains.


KEA3 of Arabidopsis thaliana


Chloroplastic K+ efflux antiporter 2, AtKEA2. Cation preference:  K+ > Cs+ > Li+ > Na+ (Aranda-Sicilia et al. 2012).  The N-terminal hydrophilic domain show sequence similarity to members of the MPA1-C family (8.A.3.1.2). Localizes to the chloroplast inner envelope membrane and plays a role in chloroplast integrity (Kunz et al. 2014). It is up-regulated under salt stress conditions (Yang et al. 2018).


KEA2 of Arabidopsis thaliana


K+ efflux antiporter 5 (AtKEA5)


KEA5 of Arabidopsis thaliana


Glutathione-regulated potassium-efflux system, KefB of 416 aas and 13 TMSs.

KefB of Helicobacter pylori


TC#NameOrganismal TypeExample
2.A.37.2.1Na+:H+ antiporter, NapA Bacteria NapA of Enterococcus hirae

The Na+/H+-K+ antiporter, GerN (spore germination protein-N) (Southworth et al., 2001).

Gram-positive bacteria

GerN of Bacillus cereus


Spore germination protein, GrmA. PTS IIA-like nitrogen-regulatory protein modulated sodium/hydrogen exchanger.

Gram-positive bacteria

GrmA of Bacillus megaterium

2.A.37.2.4The high-affinity (Km(Na+)=0.7 mM) Na+(Li+):H+ thylakoid membrane antiporter, NhaS3 (essential for growth; promotes Na+ resistance; expressed in the presence of high CO2 concentrations; under circadian control (Tsunekawa et al. 2009).


NhaS3 of Synechocystis sp. PCC6803


Na+/H+ exchanger of 732 aas.  The exchanger is the N-terminal domain, and the C-terminal domain is in the cl00292 superfamily of adenine nucleotide alpha hydrolases.  This superfamily includes N-type ATP PPases, ATP sulphurylases, Universal Stress Response proteins and electron transfer flavoproteins (ETF). The domain forms a apha/beta/apha fold which binds to adenosine nucleotides.


NHA homologue of Chlorobium limicola


Putative Na+:H+ antiporter of 388 aas and 10 TMSs, Nha.

Nha of Bdellovibrio bacteriovorus


Na+/H+ antiporter of 386 aas and 13 predicted TMSs, NapA. The 3-d structure is known (PDB# 4BWZ; 4BZ2; 4BZ3).  In the NapA structure, the core and dimerization domains are in different positions to those seen in the E. coli NhaA, and a negatively charged cavity is open to the outside. The extracellular cavity allows access to a strictly conserved aspartate residue thought to coordinate ion binding directly. To alternate access to this ion-binding site, however, requires a surprisingly large rotation of the core domain, some 20° against the dimerization interface (Lee et al. 2013). A  transmembrane lysine residue is essential for electrogenic transport in this and related Na+/H+ antiporters(Uzdavinys et al. 2017).

NapA of Thermus thermophilus


TC#NameOrganismal TypeExample

Bacterial CPA2 homologue, KefC, a  predicted glutathione-regulated potassium-efflux system.


CPA2 homologue of Myxococcus xanthus


Monovalent cation antiporter with CBS domain pair of 577 aas.

CPA protein of Pelobacter carbinolicus


Putative Na+:H+ antiporter of 438 aas and 13 TMSs.

NHA protein of Salinispira pacifica


TC#NameOrganismal TypeExample
2.A.37.4.1K+:H+ antiporter, Kha1 (YJL094c)Yeast Kha1 of Saccharomyces cerevisiae

Endosome and prevacuole K+:H+ antiporter, CHX17 of 820 aas and 13 putative TMSs.  Mediates potassium ion and pH homeomeostasis, thereby influencing membrane trafficking (Chanroj et al. 2011).  May also catalyze Na+/H+ antiport (Sze and Chanroj 2018).  CHX can promote the uptake of K+, increase the ratio of K+/Na+, and promote the growth of plants under K+ deficiency and treatment with NaCl solution (Guo et al. 2023). 

acquisition and homeostasis.


CHX17 of Arabidopsis thaliana (AAX49545)

2.A.37.4.3Plasma membrane K+ uptake transporter, CHX13 (Km ≈ 150μM; expressed in roots) (Zhao et al., 2008)

CHX13 of Arabidopsis thaliana (O22920)


CHX08 cation:H+ antiporter (expressed in pollen; Bock et al., 2006) (most like 2.A.37.4.3; 29% identity)


CHX08 of Arabidopsis thaliana (Q58P71)

2.A.37.4.5Cation/H(+) antiporter 23, chloroplastic (Protein CATION/H+ EXCHANGER 23) (AtCHX23)PlantsCHX23 of Arabidopsis thaliana
2.A.37.4.6Cation/H(+) antiporter 26 (Protein CATION/H+ EXCHANGER 26) (AtCHX26)PlantsCHX26 of Arabidopsis thaliana

Cation C+/H+ antiporter 1 (Protein CATION/H+ EXCHANGER 1) (AtCHX1).  CHX transporters play roles in salt tolerance in A thaliana seedlings (Guo et al. 2023). They promote the uptake of K+, increase the ratio of K+/Na+, and promote the growth of plants under K+ deficiency and treatment with NaCl solutions. Thus, CHXs are involved in K+ transport and improve plant salt tolerance by coordinating K+ acquisition and homeostasis. (Guo et al. 2023).


CHX1 of Arabidopsis thaliana


Endoplasmic reticular K+/H+ antiporter, CHX20.  Maintains pH and K+ homeostasis in guard cells. Plays a critical role in osmoregulation through the control of stomates opening.  Regulates alkaline pH-sensitive growth and influences membrane trafficking (Chanroj et al. 2011).


CHX20 of Arabidopsis thaliana


TC#NameOrganismal TypeExample
2.A.37.5.1The bidirectional K+/NH4+ transporter, AmhT (ammonium homeostasis transporter) (Fujisawa et al., 2007)BacteriaAmhTM of Bacillus pseudoforinus
AmhT (390 aas) (O50576)
AmhM (167 aas) (O50575)
2.A.37.5.2The K +/H+ antiporter, YhaTU (Fujisawa et al., 2007)BacteriaYhaTU of Bacillus subtilis
YhaT (165 aas) (O07535)
YhaU (408 aas) (O07536)

TC#NameOrganismal TypeExample