1.A.14 The Calcium Transporter A (CaTA) Family (formerly the Testis-Enhanced Gene Transfer (TEGT) Family)
The CaTA family (also called the BI-1/YccA family; formerly the TEGT family (SwissProt family UPF0005; Prosite entry PDOC00957)) includes members represented in all three domains of life. One of these proteins, TEGT or the Bax Inhibitor-1 (TC# 1.A.14.1.1), has a C-terminal domain that forms a Ca2+-permeable channel (Bultynck et al., 2011). These proteins are about 200-250 residues in length and exhibit 7 TMSs. They include the testis-enhanced gene transfer proteins of mammals which are expressed at high levels in the testis, the putative glutamate/aspartate binding proteins of plants and animals, the YccA protein of E. coli and the YetJ protein of Bacillus subtilis. They are distantly related to the ionotropic glutamate-binding protein of the N-methyl D-aspartate (NMDA) receptor of man. Homologues include a putative cold shock inducible protein and a SecY stabilizing protein (van Stelten et al., 2009). Bacterial CaTA (BI-1) domains are found in 'fusion' proteins of histidine sensor kinases, diguanylate cyclases and proteins with ABC2-like P-loop ATPase domains. Transmembrane BAX Inhibitor-1 Motif-containing (TMBIM) proteins that mediate Ca2+ homeostasis and cell death have been reviewed (Liu 2017).
The Transmembrane BAX Inhibitor Motif containing (TMBIM) superfamily, divided into BAX Inhibitor (BI) and Lifeguard (LFG) families, comprises a group of cytoprotective cell death regulators conserved in prokaryotes and eukaryotes. Gamboa-Tuz et al. 2018 identified 685 TMBIM proteins in 171 organisms from Archaea, Bacteria, and Eukarya, and provided a phylogenetic overview of the whole TMBIM superfamily. A bacterial member of the CaTA family has been partially characterized. This is the YbhL protein of E. coli. It is 234 aas long, exhibits 7 putative TMSs and may stimulate glucose (and fructose?) uptake or metabolism in E. coli. It plays a role in preventing E. coli cell death in the stationary phase of growth (M. Inouye, personal communication).
Homologues are found in a variety of Gram-negative and Gram-positive bacteria, yeast, fungi, plants, animals and viruses. The E. coli genome encodes three paralogues, YbhL, YbhM and YccA. Distant homologues found in Drosophilia melanogaster and the rat are the N-methyl-D-aspartate receptor-associated protein (NMDARAI) (203 aas; pirS53708) and the N-methyl-D-aspartate receptor glutamate binding chain (516 aas; pirS19586), respectively. Two others are the rat neural membrane protein 35 (NMP35) (gbAF044201) and the Arabidopsis thaliana Bax inhibitor-1 (BI-1) protein capable of suppressing Bax-induced cell death in yeast (S. cerevisiae) (247 aas; gbAB025927). Most of the more closely related homologues of the E. coli SAD protein are of 200-250 aas.
Bax Inhibitor-1 (BI-1) is an ER-localized protein that protects against apoptosis and ER stress. BI-1 has been proposed to modulate ER Ca2+ homeostasis by acting as a Ca2+-leak channel. Based on experimental determination of the BI-1 topology, Bultynck et al. (2011) proposed that its C-terminal α-helical 20 aa peptide catalyzes Ca2+ flux both in vivo and in vitro. The Ca2+-leak properties were conserved among animal, but not plant and yeast orthologs. By mutating one of the critical aspartate residues in the proposed Ca2+-channel pore in full-length BI-1, D213 proved to be essential for BI-1 dependent ER Ca2+-leak.
Calcium homeostasis balances passive calcium leak and active calcium uptake. Human Bax inhibitor-1, BI-1, an antiapoptotic protein, is representative of a highly conserved and widely distributed family, the transmembrane Bax inhibitor motif (TMBIM) proteins. Chang et al. 2014 published crystal structures of a bacterial homolog, YetJ (TC# 1.A.14.2.3) at 1.9 Å resolution and characterized its calcium leak activity. Its seven-transmembrane-helix fold features two triple-helix sandwiches wrapped around a central C-terminal helix. Structures obtained in closed and open conformations are reversibly interconvertible by changes in the pH. A hydrogen-bonded perturbed pair of conserved aspartyl residues explains the pH dependence of this transition, and the pH regulates calcium influx in proteoliposomes. Homology models for human BI-1 provided insight into its cytoprotective activity (Chang et al. 2014).
GAAPs regulate Ca2+ levels and fluxes from the Golgi and endoplasmic reticulum, confer resistance to a broad range of apoptotic stimuli, promote cell adhesion and migration via the activation of store- operated Ca2+ entry, are essential for the viability of human cells, and affect orthopoxvirus virulence. GAAPs are oligomeric, multi-transmembrane proteins that form cation-selective ion channels that may explain the multiple functions of these proteins. Residues contributing to the ion-conducting pore have been defined and provide the first clues about the mechanistic link between these very different functions of GAAP. Although GAAPs are naturally oligomeric, they can also function as monomers (Carrara et al. 2017).
The anti-apoptotic transmembrane Bax inhibitor motif (TMBIM) containing protein family regulates Ca2+ homeostasis, cell death, and the progression of diseases including cancers. Crystal structures of the TMBIM homolog YetJ of Bacillus subtilis revealed a conserved Asp171-Asp195 dyad that regulates pH-dependent Ca2+ translocation. Guo et al. 2019 showed that BsYetJ mediates Ca2+ fluxes in permeabilized mammalian cells, and its interaction with Ca2+ is sensitive to protons and other cations. They reported crystal structures of BsYetJ in several states, revealing the flexibility of the aspartyl dyad in a closed state and a pore-opening mechanism. Functional studies showed that the dyad is responsible for both Ca2+ affinity and pH dependence. Computational simulations suggested that protonation of Asp171 weakens its interaction with Arg60, leading to an open state.
The generalized reaction catalyzed by TEGT channels is:
Cations (out) ⇌ cations (in)
The Bax Inhibitor-1, BI-1 of 311 aas (or 237 aas; P55061) and 6 TMSs; it is also called the testis-enhanced gene transcript (TEGT) protein or the transmembrane BAX inhibitor motif-containing protein 6 (TMBIM6). It forms an ER, pH-sensitive, cation-selective, Ca2+-permeable leak channel (Bultynck et al., 2011; Chang et al. 2014). Residues that contribute to the ion-conducting pore and affect apoptosis, cell adhesion and migration independently have been identified (Carrara et al. 2015). The TMBIM6 calcium leak channel activity negatively regulates autophagy and autophagosome formation, influencing cardovascular traits (Swain et al. 2020). It enhances autophagy through regulation of lysosomal calcium (Kim et al. 2020). A TMBIM6 deficiency enhances susceptibility to ER stress due to inhibition of the ER stress sensor IRE1alpha. Its overexpression improves glucose metabolism, and knockout mice develop obesity (Philippaert et al. 2020). TMBIM6 knockout mice feature high glucose-stimulated insulin secretion in vivo. This coincides with profound changes in glucose-mediated Ca2+ regulation in isolated pancreatic beta cells and increases levels of IRE1alpha levels. TMBIM6-mediated metabolic alterations are mainly caused by its role as a Ca2+ release channel in the ER. Thus, TMBIM6(-/-) leads to obesity and hepatic steatosis by blocking Ca2+ transport (Philippaert et al. 2020). The mammalian Transmembrane BAX Inhibitor Motif (TMBIM) protein family in humans consists of six evolutionarily conserved hydrophobic proteins that affect programmed cell death and the regulation of intracellular calcium levels (Zhang et al. 2021). There are seven TMBIM family members in Drosophila melanogaster. Tmbim5 and 6 are essential for fly development and survival but affect cell survival through different mechanisms (Zhang et al. 2021). It prevents VDAC1 multimerization and improves mitochondrial quality control to reduce sepsis-related myocardial injury (Zhou et al. 2023).
BI-1 or TEGT of Homo sapiens (P55061)
Uncharacterized protein of 304 aas and 7 TMSs.
UP of Trypanosoma cruzi marinkellei
Uncharacterized protein of 238 aas and 7 TMSs
UP of Babesia microti
Uncharacterized protein of 317 aas and 7 TMSs
UP of Emiliania huxleyi
Growth hormone-inducible membrane protein of 345 aas and 8 putative TMSs
GH-inducible membrahe protein of Anas platyrhynchos (Mallard) (Anas boschas)
Putative Bax inhibitor of 213 aas and 7 TMSs
Putative Bax inhibitor of Entamoeba histolytica
The YccA protein, an inhibitor of FtsH. May share a similar mechanism of action as BI-1 in regulation apoptsis upon prolonged secretion stress (van Stelten et al., 2009).
YccA of E. coli (P0AAC6)
The YbhL (AceP) protein. Possibly a pmf-dependent acetate uptake transporter. [14C]Acetate uptake was inhibited by CCCP as well as cold acetate, serine, α-ketoglutarate, lactate, and succinate (M. Inouye, personal communication).
YbhL of E. coli (P0AAC4)
The 7 TMS proton-sensitive Ca2+ leak channel, YetJ. The activity and high resolution 3-d structure have been determined (Chang et al. 2014). BsYetJ in lipid nanodiscs is structurally different from those crystallized in detergents. Li et al. 2020 showed that the BsYetJ conformation is pH-sensitive in the apo state (lacking calcium), whereas in a calcium-containing solution, it is stuck in an intermediate state, inert to pH changes. Only when the transmembrane calcium gradient is established can the calcium-release activity of holo-BsYetJ occur and be mediated by pH-dependent conformational changes, suggesting a dual gating mechanism. Conformational substates involved in the process and a key residue, D171, relevant to the gating of calcium were identified. Thus, BsYetJ/TMBIM6 is a pH-dependent, voltage-gated calcium channel (Li et al. 2020). The transmembrane BAX inhibitor-1-containing motif 6 (TMBIM6) protein may modulate apoptosis by regulating calcium homeostasis in the endoplasmic reticulum (ER). Lan et al. 2023 investigated all negatively charged residues in BsYetJ, a bacterial homolog of TMBIM6. They reconstituted BsYetJ in membrane vesicles with a lipid composition similar to that of the ER. The charged residues E49 and R205 work together as a major gate, regulating calcium conductance in these ER-like lipid vesicles. However, these residues become largely inactive when reconstituted in other lipid environments. D195 acts as a minor filter compared to the E49-R205 dyad (Lan et al. 2023).
YetJ of Bacillus subtilis (O31539)
Uncharacterized protein, YbhM, of 237 aas and 7 TMSs. The ybhM gene is adjacent to the homologous ybhL gene (TC# 1.A.14.2.2), and another homologous gene is inbetween these two; these two or three genes could function together as a single transporter.
YbhM of E. coli
Protein of 234 aas and 7 TMSs encoded by a gene between and homologous to YbhL and YbhM. In the Pfam family Bax1-I.
Bax1-I protein of E. coli
Uncharacterized protein of 227 aas and 7 TMSs
UP of Streptococcus sanguinis
Bax inhibitor-1, BI1/YccA homologue of 245 aas and 7 TMSs in a 1 + 1 + 2 + 2 + 1 TMS arrangement. BrBI is a bacterial cytoprotective protein involved in membrane homeostasis, cell division, and stress resistance in Brucella suis (Zhang et al. 2021).
BI-1 of Brucella suis
The NMDA receptor glutamate binding chain. Also called Protein lifeguard-1, putative MAPK-activating protein PMO2, and transmembrane BAX inhibitor motif-containing protein 3 (TMBIM3, GRINA, LFG1, NMDARA1). The human orthologue is Q7Z429. Stimulation and block by spermine involve separate binding sites and distinct mechanisms (Jin et al. 2008).
NMDA receptor glutamate binding chain of Rattus sp. (Q63863)
The Protein Lifeguard 3 (LFG3, RECS1, Tmbim1) of 311 aas and 7 TMSs. LFG3 is a multivesicular body regulator that protects against non-alcoholic fatty liver by targeting the lysosomal degradation of Tlr4 (Zhao et al. 2017). It also protects against pathological cardiac hypertrophy by promoting the lysosomal degradation of activated TLR4 (Deng et al. 2018). RECS1 is a pH-regulated calcium channel, an activity that is essential to trigger cell death (Pihán et al. 2021).
LFG3 of Homo sapiens
Uncharacterized protein of 638 aas and 7 N-terminal TMSs
UP of Drosophila eugracilis
Viroporin, pUS21, of 243 aas and 8 TMSs. It modulates calcium ion homeostasis and protects cells against apoptosis (Luganini et al. 2018). pUS21 of human cytomegalovirus (HCMV) constitutes a TMBIM-derived viroporin that may contribute to HCMV's overall strategy to counteract apoptosis of infected cells (Luganini et al. 2023). US21, one of the 10 US12 genes (US12-US21), is a descendant of a captured cellular transmembrane BAX inhibitor motif-containing gene. It encodes a 7 TMS endoplasmic reticulum (ER)-resident viroporin (pUS21) capable of reducing the Ca2+ content of ER stores, which, in turn, protects cells against apoptosis. The US21 protein is a viral regulator of cell migration and adhesion through mechanisms involving its calcium channel activity (Luganini et al. 2023).
pUS21 of Human cytomegalovirus (strain Merlin) (HHV-5) (Human herpesvirus 5)
Lifeguard 2, LFG2, or the Brz-insensitive-long hypocotyl4 mutant ,BIL4, of 239 aas and 7 TMSs. BIL4 regulates cell elongation and Brassinosteroid (BRs; plant steroid hormones) signaling, in part via the regulation of BRI1 localization (Yamagami et al. 2017).
BIL4 of Arabidopsis thaliana
GRINA (Lifguard 1, LFG1, NMDARA1, TMBIM3) has 371 aas and 7 C-terminal TMSs. It is expressed in 218 organ(s) with highest expression in the right hemisphere of the cerebellum. It is involved in ER Ca2+ ion homeostasis and regulates apoptosis. The expression of the pro-apoptotic protein Bax is upregulated, whereas the anti-apoptotic protein Bcl-2 is downregulated in GRINA silenced cells (Xu et al. 2018). Grina/TMBIM3 modulates NMDA receptors and voltage-gated CaV2.2 Ca2+ channels (TC# 1.A.1.11.9) in a G-protein-like manner (Mallmann et al. 2019). GRINA encodes the ionotropic glutamate receptor TMBIM3 (transmembrane BAX inhibitor 1 motif-containing protein family member 3), which regulates cell survival (Rice et al. 2019).
GRINA of Homo sapiens
Tmbim3a or Grinaa of 363 aas and 7 C-terminal TMSs. A deficiency in Tmbim3a/Grinaa initiates cold-induced ER stress and cell death by activating an intrinsic apoptotic pathway in zebrafish (Chen et al. 2019).
Grinaa of Danio rerio (Zebrafish) (Brachydanio rerio)
Protein lifeguard-2 (LFG, LFG2, NMP2, NMP35, TMBIM2), Fas-apoptotic inhibitory molecule 2 (FAIM2) is of 316 aas with 7 TMSs. It is an antiapoptotic protein which protects cells uniquely from Fas-induced apoptosis and regulates Fas-mediated apoptosis in neurons by interfering with caspase-8 activation (Somia et al. 1999; Fernández et al. 2007). It is a member of the transmembrane BAX inhibitor motif-containing (TMBIM) family. The TMBIM family is comprised of six anti-apoptotic proteins that suppress cell death by regulating endoplasmic reticulum Ca2+ homeostasis. It localizes to the lysosome and facilitates autophagosome-lysosome fusion through the LC3 interaction region (Hong et al. 2020).
LFG2 of Homo sapiens
Glutamate Receptor Gr2
Gr2 of Capsaspora owczarzaki (E9CCY6)
Golgi anti-apoptotic protein, GAAP of 237 aas. Forms cation-selective channels; residues that contribute to ion-conduction and affect apoptosis, cell adhesion and migration independently have been identified (Carrara et al. 2015).
GAAP of Vaccinia virus, VacV (A2VCJ6)
Ionotropic glutamate receptor; N-methyl-D-aspartate-associated protein 1 (glutamate-binding).
Gr1 of Salmo salar (B5X2N0)
The BH3-only protein, Ynl205c (Büttner et al., 2011)
Ynl305c of Saccharomyces cerevisiae (P48558)
Protein lifeguard 4 (LFG4), also called Golgi anti-apoptotic protein (GAAP), Protein S1R, CGI-119, Transmembrane BAX inhibitor motif-containing protein 4, (TMBIM4) and Z-protein. Forms cation-selective ion channels. Residues that contribute to the ion-conducting pore and affect apoptosis, cell adhesion and migration independently of each other have been identified (Carrara et al. 2015). It's functions have been reviewed (Carrara et al. 2017). The N-methyl-D-aspartate receptor regulates the circadian clock in megakaryocytic cells and impacts cell proliferation through BMAL1 (Hearn et al. 2023).
TMBIM4 of Homo sapiens
7 TMS integral membrane protein
Uncharacterized membrane protein of Rhodopirellula baltica
Uncharacterized protein of 242 aas and 7 TMSs.
UP of Synechococcus elongatus (Anacystis nidulans R2)
Lifeguard homologue, CG3814 of 244 aas and 7 TMSs. Knockdown of CG3814/LFG in Ddc-Gal4-expressing neurons diminishes its neuroprotective ability, and results in a shortened lifespan and loss of climbing ability, phenotypes that are improved upon overexpression of the pro-survival Buffy (M'Angale and Staveley 2016).
CG3814 of Drosophila melanogaster (Fruit fly)
Viral protein HWLF3 (342 aas; 7 TMSs)
HWLF3 of human cytomegalovirus, HHV-5 (Q03307)
Viral membrane protein US14 of 286 aas and 7 TMSs.
US14 of Panine herpesvirus 2 (Chimpanzee cytomegalovirus)
Viral US18 protein of 274 aas and 7 TMSs
US18 of Human cytomegalovirus (HHV-5) (Human herpesvirus 5)
Membrane protein US12A of 250 aas and 7 TMSs
US12A of Simian cytomegalovirus
Membrane protein US19 of 240 aas and 7 TMSs.
US19 of Human cytomegalovirus (HHV-5) (Human herpesvirus 5)