1.A.14 The Calcium Transporter A (CaTA) Family (formerly the Testis-Enhanced Gene Transfer (TEGT) Family)

The CaTA family (also called the TMBIM superfamily (Gamboa-Tuz et al. 2018) and 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). Serving as a quasi-instantaneous, global readout of density and mechanical pressure, the membrane potential is integrated with signal transduction networks by affecting the conformations and clustering of proteins in the membrane, as well as the transmembrane flux of key signaling ions (Mukherjee et al. 2023).

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)