1.A.84 The Calcium Homeostasis Modulator Ca2+ Channel (CALHM-C) Family
CALHM1 (calcium homeostasis modulator 1) forms a plasma membrane ion channel that mediates neuronal excitability in response to changes in extracellular Ca2+ concentrations (Ma et al. 2012). Six human CALHM homologs exist with no homology to other proteins in humans, although CALHM1 is conserved across numerous species. Siebert et al. (2013) demonstrated that CALHM1 shares functional, quaternary and secondary structural similarities with connexins and evolutionarily distant innexins and their vertebrate pannexin homologs, all members of the 4JC superfamily in TCDB (Chou et al. 2017). A CALHM1 channel is a hexamer, comprised of six monomers, each of which possesses four transmembrane domains, cytoplasmic amino and carboxyl termini, an amino-terminal helix, and conserved extracellular cysteines (but see below). The estimated pore diameter of the CALHM1 channel is 14 Å, enabling permeation of large charged molecules. Thus, CALHMs, connexins, pannexins and innexins are structurally related protein families with shared and distinct functional properties. CALHM1 reduces the calcium content of the endoplasmic reticulum (ER) and triggers ER stress (Gallego-Sandín et al. 2011).
Killifish CALHM1 (TC# 1.A.84.1.9) of 351 aas and 5 TMSs in a 2 + 2 + 1 TMS arrangement, has been solved by cryoEM at 2.66 Å resolution (Demura et al. 2020). The human CALHM-2 (CALMH2; TC# 1.A.84.1.2) and the C. elegans CLHM-1 (CLHM1; TC# 1.A.84.1.4) were also solved at lower resolution. The Kilifish CALHM1 octameric structure reveals that the N-terminal helix forms the constriction site at the channel pore in the open state and modulates the ATP conductance. The CALHM2 undecamer and CLHM-1 nonamer structures show different oligomeric stoichiometries among CALHM homologs. The cryo-EM structures of a chimeric construct revealed that the intersubunit interactions in the transmembrane region and the TMS-intracellular domain linker define the oligomeric stoichiometry (Demura et al. 2020).
CALHM1 P86L polymorphism has been shown to be a risk factor for Alzheimer''s disease in the Chinese population (Cui et al. 2010), Japanese population (Shibata et al. 2010), and Iranian population (Aqdam et al. 2010). The CALHM1 P86L polymorphism is associated with late-onset Alzheimer''s disease in a recessive model (Boada et al., 2010). Genetic variability of the gene cluster CALHM 1-3 also manifests itself in sporadic Creutzfeldt-Jakob disease (Calero et al., 2012). Moreover, a polymorphism in CALHM1 is associated with temporal lobe epilepsy (Lv et al. 2011). The CALHM1 P86L polymorphism modulates CSF Aβ levels in cognitively healthy individuals at risk for Alzheimer''''s disease (Koppel et al. 2011). A Calhm1 knockout mouse has been generated and described (Wu et al. 2012). CALHM1 controls Ca2 -dependent MEK/ERK/RSK/MSK signaling in neurons (Dreses-Werringloer et al. 2013) and mediates purinergic neurotransmission of sweet, bitter and umami tastes (Taruno et al. 2013).
CALHM1, formerly known as FAM26C, and its C. elegans homolog, CLHM-1, are regulated by membrane voltage and extracellular Ca2+ concentration ([Ca2+]o). In the presence of physiological [Ca2+]o ( approximately 1.5 mM), CALHM1 and CLHM-1 are closed at resting membrane potentials but can be opened by strong depolarizations (Ma et al. 2015). Reducing [Ca2+]o increases channel open probability, enabling channel activation at negative membrane potentials. Thus, together, voltage and [Ca2+]o allosterically regulate CALHM channel gating.
The channels discriminate poorly among cations and anions, with signaling molecules including Ca2+ and ATP able to permeate through its pore. CALHM1 is expressed in the brain where it plays an important role in cortical neuron excitability induced by low [Ca2+]o and in type II taste bud cells in the tongue that sense sweet, bitter, and umami tastes where it functions as an essential ATP release channel to mediate nonsynaptic neurotransmitter release. CLHM-1 is expressed in C. elegans sensory neurons and body wall muscles, and its genetic deletion causes locomotion defects (Ma et al. 2015). CALHMs), through which ions and ATP permeate in a voltage-dependent manner, control neuronal excitability, taste signaling and pathologies of depression and Alzheimer's disease. Syrjanen et al. 2020 revealed the structures of two CALHMs, chicken CALHM1 and human CALHM2, by single-particle cryo-EM, which showed novel assembly of the four TMSs into channels of octamers and undecamers, respectively. Molecular dynamics simulations suggest that lipids can favorably assemble into a bilayer within the larger CALHM2 pore, but not within CALHM1
Ions and ATP permeate these CALHM channels in a voltage- dependent manner to control neuronal excitability, taste signaling and the pathologies of depression and Alzheimer's disease. (Syrjanen et al. 2020) revealed the structures of two CALHMs, chicken CALHM1 and human CALHM2, by single-particle cryo-electron microscopy (cryo-EM). These structures showed a novel assembly of four transmembrane helices into channels of octamers and undecamers, respectively. Molecular dynamics simulations suggest that lipids can favorably assemble into a bilayer within the larger CALHM2 pore, but not within CALHM1, demonstrating the potential correlation between pore size, lipid accommodation and channel activity (Syrjanen et al. 2020).
Calcium homeostasis modulators (CALHMs/CLHMs) comprise a family of pore-forming protein complexes assembling into voltage-gated, Ca2+-sensitive, nonselective channels. These complexes contain an ion-conduction pore sufficiently wide to permit the passing of ATP molecules serving as neurotransmitters. Yang et al. 2020 presented the structure of the Caenorhabditis elegans CLHM1 channel (1.A.84.1.4) in its open state, solved through single-particle cryo-EM at 3.7Å resolution. The transmembrane region of the channel structure of the dominant class shows an assembly of tenfold rotational symmetry in one layer, and its cytoplasmic region is involved in additional twofold symmetrical packing in a tail-to-tail manner. A series of amino acyl residues are critical for the regulation of the channel.
The reactions catalyezd by CALHM1 is:
Ca2+ (in) ⇌ Ca2+ (out)
ions (in) ⇌ ions (out)
ATP (in) ⇌ ATP (out)
References:
The human calcium homeostasis modulator protein 1, CALHM1 or FAM16C of 346 aas and 5 TMSs (Dreses-Werringloer et al. 2008). The P86L polymorphism increases Abeta levels and may influence Alzheimer's disease risk by interfering with CALHM1-mediated Ca2+ permeability (Dreses-Werringloer et al. 2008). The characteristics of this channel have been studied (Ma et al. 2012) and reviewed (Ma et al. 2015). Post-translational palmitoylation controls the voltage-gating and lipid raft association (Taruno et al. 2017). CALHM1 plays a role, complementary to PANX1 (TC#1.A.25.2.1), in ATP release and downstream ciliary beat frequency modulation following a mechanical stimulus in airway epithelial cells (Workman et al. 2017). CALHM1 is required for sensory perception of sweet, bitter and umami tastes. It is present in type II taste bud cells, where it plays a central role in taste perception by inducing ATP release from the cell with ATP acting as a neurotransmitter to activate afferent neural gustatory pathways. It acts both as a voltage-gated and calcium-activated ion channel mediating neuronal excitability in response to changes in extracellular Ca2+ concentration (Bhat et al. 2021). It has poor ion selectivity and forms a wide pore (around 14 Å) that mediates permeation of Ca2+, Na+ and K+, as well as monovalent anions. It acts as an activator of the ERK1 and ERK2 cascade and triggers endoplasmic reticulum stress by reducing the calcium content of the ER (Gallego-Sandín et al. 2011). It may indirectly control amyloid precursor protein (APP) proteolysis and aggregated amyloid-beta (Abeta) peptide levels in a Ca2+ dependent manner (Dreses-Werringloer et al. 2008). The ATP comes from unusually large mitochondria that are adjacent to clusters of CALHM1 channels in the plasma membrane (Romanov et al. 2018). Thus, neurotransmission does not rely on vesicle formation. Intramolecular disulfide bonds for biogenesis of CALHM1 ion channels are dispensable for voltage-dependent activation (Kwon et al. 2021). Intracellular Ca2+ oscillation frequency and amplitude modulation mediate epithelial apical and basolateral membranes crosstalk (Hassan et al. 2024).
Animals
CALHM1 of Homo sapiens (Q8IU99)
CALHM1 of 346 aas and 4 or 5 TMSs. A cryo-EM structure of full-length Ca2+-free CALHM1 from Danio rerio at an overall resolution of 3.1 Å has been published (Ren et al. 2020). The structure reveals an octameric architecture with a wide pore diameter of ~20 Å, presumably representing the active conformation. The structure is substantially different from that of the isoform CALHM2, which forms both undecameric hemichannels and gap junctions. The N-terminal small helix folds back to the pore and forms an antiparallel interaction with TMS 1. Structural analysis revealed that the extracellular loop 1 region within the dimer interface may contribute to oligomeric assembly. A positive potential belt inside the pore was identified that may modulate ion permeation (Ren et al. 2020).
CALHM1 of Danio rerio (Zebrafish) (Brachydanio rerio)
The human calcium homeostasis modulator protein 2, CALHM2 or FAM16B, of 323 aas and 4 or 5 TMSs. The structures and gating mechanism of CALHM2 have been reported (Choi et al. 2019). Cryo-EM structures in the Ca2+-free active or open state and in the ruthenium red (RUR)-bound inhibited state, have been solved at 2.7 Å resolution (see also Syrjanen et al. 2020 and Demura et al. 2020. Purified CALHM2 channels form both gap junctions and undecameric hemichannels. The protomer shows a mirrored arrangement of the TMSs (helices S1-S4) relative to other channels with a similar topology, such as connexins, innexins and volume-regulated anion channels. Upon binding to RUR, a contracted pore with notable conformational changes of the pore-lining helix S1 was observed, which swings nearly 60 degrees towards the pore axis from a vertical to a lifted position. Possibly a two-section gating mechanism is operative in which the S1 helix coarsely adjusts, and the N-terminal helix fine-tunes, the pore size (Choi et al. 2019). The Kilifish CALHM1 octameric structure reveals that the N-terminal helix forms the constriction site at the channel pore in the open state and modulates the ATP conductance. The CALHM2 undecamer and CLHM-1 nonamer structures show different oligomeric stoichiometries among CALHM homologs. The cryo-EM structures of a chimeric construct revealed that the intersubunit interactions in the transmembrane region and the TMS-intracellular domain linker define the oligomeric stoichiometry (Demura et al. 2020).
Animals
CALHM2 of Homo sapiens (Q9HA72)
The human calcium homeostasis modulator protein 3, CALHM3 or FAM26A, of 344 aas and 4 TMSs/
Animals
CALHM3 of Homo sapiens (Q86XJ0)
Calcium homeostasis modulator 1 (CALHM1 or FAM26C) is the pore-forming subunit of an ion channel that mediates extracellular Ca2+ regulation of neuronal excitability (Ma et al. 2015). CALHM1 (CALHM-1 or CLHM-1) is of 329 aas and exhibits 4 or 5 TMSs. This protein forms a protein complex, assembling into voltage-gated, Ca2+-sensitive, nonselective channels. These complexes contain an ion-conduction pore sufficiently wide to permit the passing of ATP molecules serving as neurotransmitters. Calcium homeostasis modulators (CALHMs/CLHMs) comprise a family of pore-forming protein complexes assembling into voltage-gated, Ca2+-sensitive, nonselective channels. These complexes contain an ion-conduction pore sufficiently wide to permit the passing of ATP molecules serving as neurotransmitters. Yang et al. 2020 and Demura et al. 2020 presented the structure of the Caenorhabditis elegans CLHM1 channel (1.A.84.1.4) in its open state, solved through single-particle cryo-EM at 3.7Å resolution. The transmembrane region of the channel structure of the dominant class shows an assembly of tenfold rotational symmetry in one layer, and its cytoplasmic region is involved in additional twofold symmetrical packing in a tail-to-tail manner. A series of amino acyl residues are critical for the regulation of the channel. presented the structure of the channel in its open state, solved through single-particle cryo-EM at 3.7Å resolution. The transmembrane region of the channel shows an assembly of tenfold rotational symmetry in one layer, and its cytoplasmic region is involved in additional twofold symmetrical packing in a tail-to-tail manner. A series of amino acyl residues are critical for regulation of the channel (Calcium homeostasis modulators (CALHMs/CLHMs) comprise a family of pore-forming protein complexes assembling into voltage-gated, Ca2+-sensitive, nonselective channels. These complexes contain an ion-conduction pore sufficiently wide to permit the passing of ATP molecules serving as neurotransmitters. Yang et al. 2020 presented the structure of the Caenorhabditis elegans CLHM1 channel (1.A.84.1.4) in its open state, solved through single-particle cryo-EM at 3.7Å resolution. The transmembrane region of the channel structure of the dominant class shows an assembly of tenfold rotational symmetry in one layer, and its cytoplasmic region is involved in additional twofold symmetrical packing in a tail-to-tail manner. A series of amino acyl residues are critical for regulation of the channel (Yang et al. 2020).
Animals
CALHM-1 of Caenorhabditis elegans (Q18593)
CALHM4 or FAM26D of 314 aas and 4 TMSs
Animals
FAM26D of Homo sapiens (Q5JW98)
The CALHM6 or FAM26F channel protein of 315 aas and probably 5 TMSs. FAM26F (family with sequence similarity 26, member F) plays an important role in diverse immune responses (Malik et al. 2016).
CALHM6 of Homo sapiens
Calcium homeostasis modulators (CALHMs) are ATP release channels that play crucial roles in neurons including gustatory signaling and neuronal excitability. Pathologies of Alzheimer's disease and depression have been associated with the dysfunction of CALHMs (see TC# 1.A.84.1.1). CALHM5 structures, solved by cryoEM, showed an abnormally large pore channel structure assembled as an undecamer with four transmembrane helices (TMS1-TMS4), an N-terminal helix (NTH), an extracellular loop region and an intracellular C-terminal domain (CTD) that consists of three α-helices, CH1-3. The TMS1 and NTH were poorly defined among other CALHMs, but these regions were well defined in the CALHM5 channel structure (Bhat et al. 2021).
CALHM5 of Homo sapiens
Uncharacterized protein of 1457 aas with about 850 hydrophilic N-terminal aas and 8 C-terminal TMSs in a 4 + 4 arrangement.
UP of Hirundo rustica rustica
Killifish CALHM1 of 351 aas and 5 TMSs in a 2 + 2 + 1 TMS arrangement. The cryoEM structure has been determined to 2.66 Å resolution (Demura et al. 2020). The human CALHM-2 (CALMH2) and the C. elegans CLHM-1 (CLHM1) were also solved at lower resolution. The CALHM1 octameric structure reveals that the N-terminal helix forms the constriction site at the channel pore in the open state and modulates the ATP conductance. The CALHM2 undecamer and CLHM-1 nonamer structures show the different oligomeric stoichiometries among CALHM homologs. The cryo-EM structures of the chimeric construct revealed that the intersubunit interactions in the transmembrane region and the TMS-intracellular domain linker define the oligomeric stoichiometry (Demura et al. 2020).
CALHM1 of Oryzias latipes (Japanese rice fish) (Japanese killifish)
Sea anemone CALHM homologue
Animals
CALHM homologue of Nematostella vectensis
Uncharacterized protein of 304 aas and 4 TMSs.
UP of Nematostella vectensis (Starlet sea anemone)
Uncharacterized protein of 769 aas and 8 TMSs in a 4 + 4 TMS arrangement, with each 3 TMS unit followed by a hydrophilic region of about 180 aas.
UP of Stylophora pistillata
Calcium homeostasis modulator protein 5-like of 362 aas and 4 or 5 TMSs.
CALHM protein of Actinia tenebrosa
Uncharacterized protein of 356 aas and 4 or 5 TMSs.
UP of Pocillopora damicornis
Uncharacterized protein of 435 aas and 4 N-terminal TMSs (the FAM26 domain) followed by a hydrophilic region that shows sequence similarity with 9.B.96.1.1 (e-7).
UP of Pelodiscus sinensis (Chinese soft-shelled turtle)
Uncharacterized protein of 329 aas and 4 TMSs.
UP of Henneguya salminicola
Uncharacterized protein of 275 aas and 4 TM
UP of Salmo trutta (river trout)
Uncharacterized protein of 431 aas and 4 TMSs
UP of Pygocentrus nattereri (red-bellied piranha)
Uncharacterized protein of 328 aas and 4 TMSs
UP of Sander lucioperca (pike-perch)
Uncharacterized protein of 494 aas with 4 N-terminal TMSs and an long hydrophilic domain with one C-terminal TMS
UP of Oryzias latipes (Japanese medaka)
Uncharacterized protein of 268 aas and 4 TMSs
UP of Archocentrus centrarchus (flier cichlid)
Uncharacterized protein of 311 aas and 4 TMSs.
UP of Anabas testudineus (climbing perch)
Uncharacterized protein of 290 aas and 4 TMSs.
UP of Astatotilapia calliptera (eastern happy)
Uncharacterized protein of 332 aas and 4 N-terminal TMSs
UP of Erpetoichthys calabaricus (reedfish)
Uncharacterized protein of 312 aas and 4 TMSs
UP of Pomacea canaliculata
Uncharacterized protein of 385 aas and 4 N-terminal TMSs.
UP of Pomacea canaliculata
Uncharacterized protein of 278 aas and 4 TMSs. This protein shows substantial sequence similarity with TC#s 1.A.84.1.8, 1.7 and 1.5 (up to e-6).
UP of Pomacea canaliculata