2.A.106 Ca²⁺:H⁺Antiporter-2 (CaCA2) Family The PF27 family (SwissProt family UPF0016; Prosite entry PDOC00934) is a small family of proteins found in bacteria, archaea, yeast, plants and animals. They are usually 200-350 amino acyl residues long and exhibit 5-7 TMSs. Congenital Disorders of Glycosylation (CDG) are rare inherited diseases causing glycosylation defects responsible for severe growth and psychomotor retardations in patients. TMEM165 has been implicated in both Golgi vesicular trafficking and ion homeostasis. TMEM165 deficient mammalian cells or yeast cells deficient in Gtd1p, the yeast TMEM165 ortholog suggest that TMEM165 is a transporter involved in ion homeostasis (Dulary et al. 2017). Several studies indicate that TMEM165 is a Golgi localized Ca²⁺/H⁺ and/or Mn²⁺/H⁺ antiporter. Possibly TMEM165 proteins are Mn²⁺ transporters essential to achieve the correct N-glycosylation process of proteins in the secretory pathway. Defects in the human TMEM165 homologue are the cause of congenital disorder of glycosylation type 2K (CDG2K), an autosomal recessive disorder with variable phenotypes (Foulquier et al.2012). Affected individuals show psychomotor and growth retardation, and most have short stature. Other features include dysmorphism, hypotonia, eye abnormalities, acquired microcephaly, hepatomegaly, and skeletal dysplasia. Congenital disorders of glycosylation are caused by a defect in glycoprotein biosynthesis and are characterized by under-glycosylated serum glycoproteins and a wide variety of clinical features. The broad spectrum of features may reflect the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions (Foulquier et al. 2012). The Ca²⁺:H⁺Antiporter (CaCA2) Family (previous called the uncharacterized Protein Family 0016 (UPF0016), is well conserved throughout prokaryotes and eukaryotes. The yeast golgi Gcr1-dependent translation factor 1 protein (Gdt1p) contributes to Ca²⁺homeostasis. A yeast gdt1 mutant was found to be sensitive to high concentrations of Ca²⁺, and this sensitivity was suppressed by expression of human TMEM165 in yeast (Demaegd et al.2013). Patch-clamp analyses on human cells indicated that TMEM165 catalyzes Ca²⁺transport, and defects in TMEM165 affected both Ca²⁺and pH homeostasis.Gdt1p and TMEM165 are probably Golgi-localized Ca²⁺:H⁺antiporters. Modification of the Golgi Ca²⁺and pH balance could explain the glycosylation defects observed in TMEM165-deficient patients. The UPF0016 family is defined by the presence of 1 or 2 copies of the E-phi-G-D-[KR]-[TS] consensus motif in their transmembrane domain. Colinet et al. 2017 showed that 2 members of this family, the human TMEM165 and the budding yeast Gdt1p, are functionally related Ca²⁺ transporters. Mutations in TMEM165 cause a type of rare human genetic diseases called Congenital Disorders of Glycosylation. Mutations in the yeast Golgi-localized Ca²⁺ transporter, Gdt1, revealed that acidic and polar uncharged residues of the consensus motifs are involved in calcium tolerance and calcium transport activity. The E53 residue corresponds to the mutation in humans that triggers congenital disorders of glycosylation (Colinet et al. 2017). The generalized reaction catalyzed by CaCA2 family members is: Ca²⁺(cytoplasm) + H⁺(golgi lumen) → Ca²⁺(golgi lumen) + H⁺(cytoplasm)
This family belongs to the LysE Superfamily.
References:
Colinet, A.S., L. Thines, A. Deschamps, G. Flémal, D. Demaegd, and P. Morsomme. (2017). Acidic and uncharged polar residues in the consensus motifs of the yeast Ca²⁺ transporter Gdt1p are required for calcium transport. Cell Microbiol. [Epub: Ahead of Print]
Demaegd, D., F. Foulquier, A.S. Colinet, L. Gremillon, D. Legrand, P. Mariot, E. Peiter, E. Van Schaftingen, G. Matthijs, and P. Morsomme. (2013). Newly characterized Golgi-localized family of proteins is involved in calcium and pH homeostasis in yeast and human cells. Proc. Natl. Acad. Sci. USA 110: 6859-6864.
Deutschbauer, A., M.N. Price, K.M. Wetmore, W. Shao, J.K. Baumohl, Z. Xu, M. Nguyen, R. Tamse, R.W. Davis, and A.P. Arkin. (2011). Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet 7: e1002385.
Dulary, E., S. Potelle, D. Legrand, and F. Foulquier. (2017). TMEM165 deficiencies in Congenital Disorders of Glycosylation type II (CDG-II): Clues and evidences for roles of the protein in Golgi functions and ion homeostasis. Tissue Cell 49: 150-156.
Foulquier, F., M. Amyere, J. Jaeken, R. Zeevaert, E. Schollen, V. Race, R. Bammens, W. Morelle, C. Rosnoblet, D. Legrand, D. Demaegd, N. Buist, D. Cheillan, N. Guffon, P. Morsomme, W. Annaert, H.H. Freeze, E. Van Schaftingen, M. Vikkula, and G. Matthijs. (2012). TMEM165 deficiency causes a congenital disorder of glycosylation. Am J Hum Genet 91: 15-26.
Hoecker, N., D. Leister, and A. Schneider. (2017). Plants contain small families of UPF0016 proteins including the PHOTOSYNTHESIS AFFECTED MUTANT71 transporter. Plant Signal Behav 0. [Epub: Ahead of Print]
Jankauskas, S.S., F. Varzideh, U. Kansakar, G. Al Tibi, E. Densu Agyapong, J. Gambardella, and G. Santulli. (2024). Insights into molecular and cellular functions of the Golgi calcium/manganese-proton antiporter TMEM165. J. Biol. Chem. 300: 107567.
Lee, J.S., M.Y. Kim, E.R. Park, Y.N. Shen, J.Y. Jeon, E.H. Cho, S.H. Park, C.J. Han, D.W. Choi, J.J. Jang, K.S. Suh, J. Hong, S.B. Kim, and K.H. Lee. (2018). TMEM165, a Golgi transmembrane protein, is a novel marker for hepatocellular carcinoma and its depletion impairs invasion activity. Oncol Rep 40: 1297-1306.
Legrand, D., M. Herbaut, Z. Durin, G. Brysbaert, M. Bardor, M.F. Lensink, and F. Foulquier. (2023). New insights into the pathogenicity of TMEM165 variants using structural modeling based on AlphaFold 2 predictions. Comput Struct Biotechnol J 21: 3424-3436.
Schneider, A., I. Steinberger, A. Herdean, C. Gandini, M. Eisenhut, S. Kurz, A. Morper, N. Hoecker, T. Rühle, M. Labs, U.I. Flügge, S. Geimer, S.B. Schmidt, S. Husted, A.P. Weber, C. Spetea, and D. Leister. (2016). The Evolutionarily Conserved Protein PHOTOSYNTHESIS AFFECTED MUTANT71 Is Required for Efficient Manganese Uptake at the Thylakoid Membrane in Arabidopsis. Plant Cell 28: 892-910.
Snyder, N.A., M.V. Palmer, T.A. Reinhardt, and K.W. Cunningham. (2019). Milk biosynthesis requires the Golgi cation exchanger TMEM165. J. Biol. Chem. 294: 3181-3191.
Stribny, J., L. Thines, A. Deschamps, P. Goffin, and P. Morsomme. (2020). The human Golgi protein TMEM165 transports calcium and manganese in yeast and bacterial cells. J. Biol. Chem. 295: 3865-3874.
Thines, L., A. Deschamps, P. Sengottaiyan, O. Savel, J. Stribny, and P. Morsomme. (2018). The yeast protein Gdt1p transports Mn ions and thereby regulates manganese homeostasis in the Golgi. J. Biol. Chem. [Epub: Ahead of Print]
Wang, C., W. Xu, H. Jin, T. Zhang, J. Lai, X. Zhou, S. Zhang, S. Liu, X. Duan, H. Wang, C. Peng, and C. Yang. (2016). A Putative Chloroplast-Localized Ca²⁺/H⁺ Antiporter CCHA1 Is Involved in Calcium and pH Homeostasis and Required for PSII Function in Arabidopsis. Mol Plant 9: 1183-1196.
Zhang, Y., S. Newstead, and P. Sarkies. (2025). Predicting substrates for orphan solute carrier proteins using multi-omics datasets. BMC Genomics 26: 130.
Examples:
TC#	Name	Organismal Type	Example
2.A.106.1.1	The Y615 protein	Bacteria	*Y615 of Synechocystis* PCC6803**

2.A.106.1.2	Uncharacterized protein of 194 aas and 6 TMSs with two 3-TMS repeats.	Actinobacteria	UP of Streptomyces griseus

2.A.106.1.3	Uncharacterized protein of 213 aas and 6 TMSs	Chlorobi	UP of Chlorobium chlorochromatii

2.A.106.1.4	Uncharacterized protein of 192 aas probably with 6 TMSs in a 3 + 3 TMS repeat unit.	β-Proteobacteria	UP of Acidovorax ebreus

2.A.106.1.5	Chloroplast thylakoid GDT-1-like protein or photosynthesis-affected protein-71, PAM71 or CCHA1 of 370 aas with 6 TMSs in a 3 + 3 TMS arrangement. It takes up Mn²⁺ and influences both Mn²⁺ and Ca²⁺ homeostasis in the chloroplast. It is necessary for photosystem II function due to its Mn²⁺ uptake activity (Schneider et al. 2016; Hoecker et al. 2017). It is an Mn²⁺/H⁺ exchanger, which transport Mn²⁺from the chloroplast stroma into the acidic thylakoid lumen (Schneider et al. 2016). It might be a chloroplast-localized Ca²⁺/H⁺ antiporter as well (Wang et al. 2016) since it regulates Ca²⁺, Mn²⁺ and pH homeostasis and is required for chloroplast development.		PAM71 orCCHA1 of Arabidopsis thaliana

2.A.106.1.6	*Manganese (Mn²⁺):proton exchanger, CGLD1, of 340 aas (Schneider et al.* 2016; ).**		CGLD1 of Chlamydomonas reinhardtii (Chlamydomonas smithii)

2.A.106.1.7	*Photosynthesis-affected mutant 71, PAM71 homologue, PAM71-HL, of 359 aas and 7 TMSs (Hoecker et al.* 2017). Probably a manganese ion transporter; a member of the UPF0016 family.**		*PAM71-HL of Arabidopsis thaliana* (Mouse-ear cress)**

2.A.106.1.8	*Putative DL-lactate uptake porter of 184 aas and 6 - 7 TMSs (Deutschbauer et al.* 2011).**		SO_1071 of Shewanella oneidensis

Examples:
TC#	Name	Organismal Type	Example
2.A.106.2.1	The PFT27 protein of 323 aas with 7 putative TMSs in a 1 + 3 + 3 TMS arrangement, in which the 3 TMS unit is possibly a repeat seqence.	Animals	PFT27 of Mus musculus

2.A.106.2.2	Ca²⁺/Mn²⁺/Mg²⁺:H⁺antiporter, TMEM165 (PT27; TPARL; SLC64A1) of 324 aas and 7 TMSs in a 1 (N-terminal) + 3 + 3 TMS arrangement (Demaegd et al. 2013). It may be both a Ca²⁺:H⁺ and a Mn²⁺:H⁺ antiporter (Dulary et al. 2016; Stribny et al. 2020), catalyzing uptake of Mn²⁺ from the cytoplasm into the golgi lumen. TMEM165 has been linked to congenital disorders of glycosylation (CDG) (Foulquier et al. 2012). It may influence glycosylation due to its Mn²⁺ transport activity that regulates Mn²⁺ homeostasis in the golgi (Thines et al. 2018). TMEM165 is also required for milk production (Snyder et al. 2019). In humans, both Ca²⁺ and Mn²⁺ are required for proper protein glycosylation in cells (Stribny et al. 2020). TMEM165, a Golgi transmembrane protein, is a novel marker for hepatocellular carcinoma, and its depletion impairs invasion activity (Lee et al. 2018). The pathogenicity of TMEM165 variants using structural modeling based on AlphaFold 2 predictions has been presented (Legrand et al. 2023). Mutations in the gene encoding TMEM165 are a cause of a new type of congenital disorder of glycosylation (CDG) (Jankauskas et al. 2024). Comprehensive studies of TMEM165 in different model systems, including mammals, yeast, and fish uncovered the new realm of Mn²⁺ homeostasis regulation. TMEM165 was shown to act as a Ca²⁺/Mn²⁺:H⁺ antiporter in the medial- and trans-Golgi network, pumping the metal ions into the Golgi lumen and protons outside. Disruption of TMEM165 antiporter activity results in defects in N- and O-glycosylation of proteins and glycosylation of lipids. Impaired glycosylation of TMEM165-CDG arises from a lack of Mn²⁺ within the Golgi. Nevertheless, Mn²⁺ insufficiency in the Golgi is compensated by the activity of the ATPase SERCA2. TMEM165 turnover has also been found to be regulated by the Mn²⁺ cytosolic concentration. Besides causing CDG, the functional involvement of TMEM165 in several other pathologies including cancer and mental health disorders has been described. This systematic review summarizes the available information on TMEM165 molecular structure, cellular function, and its roles in health and disease (Jankauskas et al. 2024). It may catalyze Ca²⁺ import into lysosomes (Zhang et al. 2025).	Animals	*TMEM165 of Homo sapiens* (Q9HC07)**

2.A.106.2.3	Golgi Ca²⁺:H⁺ and Mn²⁺:H⁺ antiporter, Gdt1 (GCR-1-dependent translation factor 1) or TMEM165 (Demaegd et al., 2013). Involved in ion homeostasis (Dulary et al. 2016), specifically Mn²⁺ homeostasis (Thines et al. 2018).	Yeast	*Gdt1 of Saccharomyces cerevisiae* (P38301)**

2.A.106.2.4	The YD68 protein	Yeast	YD68 of Schizosaccharomyces pombe

2.A.106.2.5	Golgi Ca²⁺ ion homeostasis protein, TM protein PFT27, of 515 aas and 8 putative TMSs in a 2 (N-terminal) + 3 (middle) + 3 (C-terminal) TMSs.		Transmembrane protein PFT27 of Pyrenophora tritici-repentis (Wheat tan spot fungus) (Drechslera tritici-repentis)

Examples:
TC#	Name	Organismal Type	Example
2.A.106.3.1	3 TMS homologue of 89 aas	Spirochaetes	3 TMS homologue of Leptonema illini

2.A.106.3.2	3 TMS homologue of 90 aas	δ-Proteobacteria	3 TMS homologue of Bdellovibrio bacteriovorus

Examples:
TC#	Name	Organismal Type	Example
2.A.106.4.1	Uncharacterized protein of 235 aas	Archaea	UP of Haloarcula japonica

Examples:
TC#	Name	Organismal Type	Example