TCDB is operated by the Saier Lab Bioinformatics Group

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 associated with 1.A.84 family:

Aqdam, M.J., K. Kamali, M. Rahgozar, M. Ohadi, M. Manoochehri, A. Tahami, L. Bostanshirin, and H.R. Khorshid. (2010). Association of CALHM1 Gene Polymorphism with Late Onset Alzheimer's Disease in Iranian Population. Avicenna J Med Biotechnol 2: 153-157. 23408664
Boada, M., C. Antúnez, J. López-Arrieta, J.J. Galán, F.J. Morón, I. Hernández, J. Marín, P. Martínez-Lage, M. Alegret, J.M. Carrasco, C. Moreno, L.M. Real, A. González-Pérez, L. Tárraga, and A. Ruiz. (2010). CALHM1 P86L polymorphism is associated with late-onset Alzheimer's disease in a recessive model. J Alzheimers Dis 20: 247-251. 20164592
Calero, O., M.J. Bullido, J. Clarimón, R. Hortigüela, A. Frank-García, P. Martínez-Martín, A. Lleó, M.J. Rey, I. Sastre, A. Rábano, J. de Pedro-Cuesta, I. Ferrer, and M. Calero. (2012). Genetic variability of the gene cluster CALHM 1-3 in sporadic Creutzfeldt-Jakob disease. Prion 6: 407-412. 22874670
Choi, W., N. Clemente, W. Sun, J. Du, and W. Lü. (2019). The structures and gating mechanism of human calcium homeostasis modulator 2. Nature 576: 163-167. 31776515
Chou, A., A. Lee, K.J. Hendargo, V.S. Reddy, M.A. Shlykov, H. Kuppusamykrishnan, A. Medrano-Soto, and M.H. Saier, Jr. (2017). Characterization of the Tetraspan Junctional Complex (4JC) superfamily. Biochim. Biophys. Acta. Biomembr 1859: 402-414. 27916633
Cui, P.J., L. Zheng, L. Cao, Y. Wang, Y.L. Deng, G. Wang, W. Xu, H.D. Tang, J.F. Ma, T. Zhang, J.Q. Ding, Q. Cheng, and S.D. Chen. (2010). CALHM1 P86L polymorphism is a risk factor for Alzheimer's disease in the Chinese population. J Alzheimers Dis 19: 31-35. 20061624
Demura, K., T. Kusakizako, W. Shihoya, M. Hiraizumi, K. Nomura, H. Shimada, K. Yamashita, T. Nishizawa, A. Taruno, and O. Nureki. (2020). Cryo-EM structures of calcium homeostasis modulator channels in diverse oligomeric assemblies. Sci Adv 6: eaba8105. 32832629
Dreses-Werringloer U., Vingtdeux V., Zhao H., Chandakkar P., Davies P. and Marambaud P. (2013). CALHM1 controls the Ca(2)(+)-dependent MEK, ERK, RSK and MSK signaling cascade in neurons. J Cell Sci. 126(Pt 5):1199-206. 23345406
Dreses-Werringloer, U., J.C. Lambert, V. Vingtdeux, H. Zhao, H. Vais, A. Siebert, A. Jain, J. Koppel, A. Rovelet-Lecrux, D. Hannequin, F. Pasquier, D. Galimberti, E. Scarpini, D. Mann, C. Lendon, D. Campion, P. Amouyel, P. Davies, J.K. Foskett, F. Campagne, and P. Marambaud. (2008). A polymorphism in CALHM1 influences Ca2+ homeostasis, Abeta levels, and Alzheimer's disease risk. Cell 133: 1149-1161. 18585350
Gallego-Sandín, S., M.T. Alonso, and J. García-Sancho. (2011). Calcium homoeostasis modulator 1 (CALHM1) reduces the calcium content of the endoplasmic reticulum (ER) and triggers ER stress. Biochem. J. 437: 469-475. 21574960
Koppel, J., F. Campagne, V. Vingtdeux, U. Dreses-Werringloer, M. Ewers, D. Rujescu, H. Hampel, M.L. Gordon, E. Christen, J. Chapuis, B.S. Greenwald, P. Davies, and P. Marambaud. (2011). CALHM1 P86L polymorphism modulates CSF Aβ levels in cognitively healthy individuals at risk for Alzheimer's disease. Mol Med 17: 974-979. 21629967
Lv, R.J., J.S. He, Y.H. Fu, X.Q. Shao, L.W. Wu, Q. Lu, L.R. Jin, and H. Liu. (2011). A polymorphism in CALHM1 is associated with temporal lobe epilepsy. Epilepsy Behav 20: 681-685. 21439911
Ma, Z., A.P. Siebert, K.H. Cheung, R.J. Lee, B. Johnson, A.S. Cohen, V. Vingtdeux, P. Marambaud, and J.K. Foskett. (2012). Calcium homeostasis modulator 1 (CALHM1) is the pore-forming subunit of an ion channel that mediates extracellular Ca2+ regulation of neuronal excitability. Proc. Natl. Acad. Sci. USA 109: E1963-1971. 22711817
Ma, Z., J.E. Tanis, A. Taruno, and J.K. Foskett. (2015). Calcium homeostasis modulator (CALHM) ion channels. Pflugers Arch. [Epub: Ahead of Print] 26603282
Malik, U., A. Javed, A. Ali, and K. Asghar. (2016). Structural and functional annotation of human FAM26F: A multifaceted protein having a critical role in the immune system. Gene. [Epub: Ahead of Print] 27784631
Ren, Y., T. Wen, Z. Xi, S. Li, J. Lu, X. Zhang, X. Yang, and Y. Shen. (2020). Cryo-EM structure of the calcium homeostasis modulator 1 channel. Sci Adv 6: eaba8161. 32832630
Romanov, R.A., R.S. Lasher, B. High, L.E. Savidge, A. Lawson, O.A. Rogachevskaja, H. Zhao, V.V. Rogachevsky, M.F. Bystrova, G.D. Churbanov, I. Adameyko, T. Harkany, R. Yang, G.J. Kidd, P. Marambaud, J.C. Kinnamon, S.S. Kolesnikov, and T.E. Finger. (2018). Chemical synapses without synaptic vesicles: Purinergic neurotransmission through a CALHM1 channel-mitochondrial signaling complex. Sci Signal 11:. 29739879
Shibata, N., B. Kuerban, M. Komatsu, T. Ohnuma, H. Baba, and H. Arai. (2010). Genetic association between CALHM1, 2, and 3 polymorphisms and Alzheimer's disease in a Japanese population. J Alzheimers Dis 20: 417-421. 20164573
Siebert, A.P., Z. Ma, J.D. Grevet, A. Demuro, I. Parker, and J.K. Foskett. (2013). Structural and Functional Similarities of Calcium Homeostasis Modulator 1 (CALHM1) Ion Channel with Connexins, Pannexins, and Innexins. J. Biol. Chem. 288: 6140-6153. 23300080
Syrjanen, J.L., K. Michalski, T.H. Chou, T. Grant, S. Rao, N. Simorowski, S.J. Tucker, N. Grigorieff, and H. Furukawa. (2020). Structure and assembly of calcium homeostasis modulator proteins. Nat Struct Mol Biol 27: 150-159. 31988524
Taruno A., Vingtdeux V., Ohmoto M., Ma Z., Dvoryanchikov G., Li A., Adrien L., Zhao H., Leung S., Abernethy M., Koppel J., Davies P., Civan MM., Chaudhari N., Matsumoto I., Hellekant G., Tordoff MG., Marambaud P. and Foskett JK. (2013). CALHM1 ion channel mediates purinergic neurotransmission of sweet, bitter and umami tastes. Nature. 495(7440):223-6. 23467090
Taruno, A., H. Sun, K. Nakajo, T. Murakami, Y. Ohsaki, M.A. Kido, F. Ono, and Y. Marunaka. (2017). Post-translational palmitoylation controls the voltage gating and lipid raft association of the CALHM1 channel. J. Physiol. [Epub: Ahead of Print] 28734079
Workman, A.D., R.M. Carey, B. Chen, C.J. Saunders, P. Marambaud, C.H. Mitchell, M.G. Tordoff, R.J. Lee, and N.A. Cohen. (2017). CALHM1-Mediated ATP Release and Ciliary Beat Frequency Modulation in Nasal Epithelial Cells. Sci Rep 7: 6687. 28751666
Wu, J., S. Peng, R. Wu, Y. Hao, G. Ji, and Z. Yuan. (2012). Generation of Calhm1 knockout mouse and characterization of calhm1 gene expression. Protein Cell 3: 470-480. 22723178
Yang, W., Y. Wang, J. Guo, L. He, Y. Zhou, H. Zheng, Z. Liu, P. Zhu, and X.C. Zhang. (2020). Cryo-electron microscopy structure of CLHM1 ion channel from Caenorhabditis elegans. Protein. Sci. [Epub: Ahead of Print] 32557855