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1.A.3 The Ryanodine-Inositol 1,4,5-triphosphate Receptor Ca2+ Channel (RIR-CaC) Family

Ryanodine (Ry)-sensitive and inositol 1,4,5-triphosphate (IP3)-sensitive Ca2+-release channels function in the release of Ca2+ from intracellular storage sites in animal cells and thereby regulate various Ca2+-dependent physiological processes (Van Petegem 2012). They consist of (1) an N-terminal ligand binding domain, (2) a central modulatory domain and (3) a C-terminal channel-forming domain. The 3-D structure (2.2 Å) of the inositol 1,3,5-triphosphate receptor of an IP3 receptor has been solved (Bosanac et al., 2002). Structural and functional conservation of key domains in InsP(3) and ryanodine receptors has been reviewed (Seo et al., 2012).

Ry receptors occur primarily in muscle cell sarcoplasmic reticular (SR) membranes, and IP3 receptors occur primarily in brain cell endoplasmic reticular (ER) membranes where they effect release of Ca2+ into the cytoplasm upon activation (opening) of the channel. They are redox sensors, possibly providing a partial explanation for how they control cytoplasmic Ca2+. Ry receptors have been identified in heart mitochondria, and these provide the main pathway for Ca2+ entry (Beutner et al., 2001). Sun et al. (2011) have demonstrated oxygen-coupled redox regulation of the skeletal muscle ryanodine receptor-Ca2+ release channel (RyR1) by NADPH oxidase 4.

The Ry receptors are activated as a result of the activity of dihydropyridine-sensitive Ca2+ channels. Ry receptors, IP3 receptors, and dihydropyridine-sensitive Ca2+ channels (TC#1.A.1.11.2) are members of the voltage-sensitive ion channel (VIC) superfamily (TC#1.A.1). Dihydropyridine-sensitive channels are present in the T-tubular systems of muscle tissues. Ry receptor 2 dysfunction leads to arrhythmias, alterred myocyte contraction during the process of EC (excitation-contraction) coupling, and sudden cardiac death (Thomas et al., 2007). Neomycin is a RyR blocker which serves as a pore plug and a competitive antagonist at a cytoplasmic Ca2+ binding site that causes allosteric inhibition (Laver et al., 2007).

Ry receptors are homotetrameric complexes with each subunit exhibiting a molecular size of over 500,000 daltons (about 5,000 amino acyl residues). They possess C-terminal domains with six putative transmembrane α-helical spanners (TMSs). Putative pore-forming sequences occur between the fifth and sixth TMSs as suggested for members of the VIC family. Recently an 8 TMS topology with four hairpin loops has been suggested (Du et al., 2002). The large N-terminal hydrophilic domains and the small C-terminal hydrophilic domains are localized to the cytoplasm. Low resolution 3-dimensional structural data are available. Mammals possess at least three isoforms which probably arose by gene duplication and divergence before divergence of the mammalian species. Homologues are present in Drosophila melanogaster and Caenorabditis elegans.

Tetrameric cardiac and skeletal muscle sarcoplasmic reticular ryanodine receptors (RyR) are large (~2.3 MDa). The complexes include signaling proteins such as 4 FKBP12 molecules, protein kinases, phosphatases, etc. They modulate the activity of and the binding of immunophilin to the channel. FKBP12 is required for normal gating as well as coupled gating between neighboring channels. PKA phosphorylation of RyR dissociates FKBP12 yielding increased Ca2+ sensitivity for activation, part of the excitation-contraction (fight or flight) response (Gaburjakova et al., 2001).

IP3 receptors resemble Ry receptors in many respects (Mikoshiba, 2012). (1) They are homotetrameric complexes with each subunit exhibiting a molecular size of over 300,000 daltons (about 2,700 amino acyl residues). (2) They possess C-terminal channel domains that are homologous to those of the Ry receptors. (3) The channel domains possess six putative TMSs and a putative channel lining region between TMSs 5 and 6. (4) Both the large N-terminal domains and the smaller C-terminal tails face the cytoplasm. (5) They possess covalently linked carbohydrate on extracytoplasmic loops of the channel domains. (6) They have three currently recognized isoforms (types 1, 2, and 3) in mammals which are subject to differential regulation and have different tissue distributions. They co-localize with Orai channels (1.A.52) in pancreatic acinar cells (Lur et al., 2011).

IP3 receptors possess three domains: N-terminal IP3-binding domains, central coupling or regulatory domains and C-terminal channel domains. Channels are activated by IP3 binding, and like the Ry receptors, the activities of the IP3 receptor channels are regulated by phosphorylation of the regulatory domains, catalyzed by various protein kinases. They predominate in the endoplasmic reticular membranes of various cell types in the brain but have also been found in the plasma membranes of some nerve cells derived from a variety of tissues.

Specific residues in the putative pore helix, selectivity filter and S6 transmembrane helix of the IP3 receptor, have been mutated (Schug et al., 2008) in order to examine their effects on channel function. Mutation of 5 of 8 highly conserved residues in the pore helix/selectivity filter region inactivated the channel. Channel function was also inactivated by G2586P and F2592D mutations. These studies defined the pore-forming segment in IP (Schug et al., 2008).

The channel domains of the Ry and IP3 receptors comprise a coherent family that shows apparent structural similarities as well as sequence similarity with proteins of the VIC family (TC #1.A.1). The Ry receptors and the IP3 receptors cluster separately on the RIR-CaC family tree. They both have homologues in Drosophila. Based on the phylogenetic tree for the family, the family probably evolved in the following sequence: (1) A gene duplication event occurred that gave rise to Ry and IP3 receptors in invertebrates. (2) Vertebrates evolved from invertebrates. (3) The three isoforms of each receptor arose as a result of two distinct gene duplication events. (4) These isoforms were transmitted to mammals before divergence of the mammalian species.

The generalized transport reaction catalyzed by members of the RIR-CaC family following channel activation is:

Ca2+ (out, or sequestered in the ER or SR) → Ca2+ (cell cytoplasm).

This family belongs to the: VIC Superfamily.

References associated with 1.A.3 family:

Beutner, G., V.K. Sharma, D.R. Giovannucci, D.I. Yule and S.-S. Sheu (2001). Identification of a ryanodine receptor in rat heart mitochondria. J. Biol. Chem. 276: 21482-21488. 11297554
Bosanac, I., J.-R. Alattia, T.K. Mal, J. Chan, S. Talarico, F.K. Tong, K.I. Tong, F. Yoshikawa, T. Furuichi, M. Iwai, T. Michikawa, K. Mikoshiba, and M. Ikura. (2002). Structure of the inositol 1,4,5-trisphosphate receptor binding core in complex with its ligand. Nature 420: 696-700. 12442173
Chelu, M.G., and X.H. Wehrens. (2007). Sarcoplasmic reticulum calcium leak and cardiac arrhythmias. Biochem. Soc. Trans. 35: 952-956. 17956253
Docampo, R., S.N. Moreno, and H. Plattner. (2013). Intracellular calcium channels in protozoa. Eur J Pharmacol. [Epub: Ahead of Print] 24291099
Du, G.G., B. Sandhu, B.K. Khanna, Z.H. Guo, and D.H. MacLennan. (2002). Topology of the Ca2+ release channel of skeletal muscle sarcoplasmic reticulum (RyR1). Proc. Natl. Acad. Sci. USA 99: 16725-16730. 12486242
Gaburjakova, M., J. Gaburjakova, S. Reiken, F. Huang, S.O. Marx, N. Rosemblit and A.R. Marks (2001). FKBP12 binding modulates ryanodine receptor channel gating. J. Biol. Chem. 276: 16931-16935. 11279144
Hasan, G. and M. Rosbash. (1992). Drosophila homologues of two mammalian Ca2+-release channels: identification and expression patterns of the inositol 1,4,5-triphosphate and the ryanodine receptor genes. Development 116: 967-975. 1338312
Jones, P.P., X. Meng, B. Xiao, S. Cai, J. Bolstad, T. Wagenknecht, Z. Liu, and S.R. Chen. (2008). Localization of PKA phosphorylation site, Ser(2030), in the three-dimensional structure of cardiac ryanodine receptor. Biochem. J. 410: 261-270. 17967164
Kato, K., S. Kiyonaka, Y. Sawaguchi, M. Tohnishi, T. Masaki, N. Yasokawa, Y. Mizuno, E. Mori, K. Inoue, I. Hamachi, H. Takeshima, and Y. Mori. (2009). Molecular characterization of flubendiamide sensitivity in the lepidopterous ryanodine receptor Ca2+ release channel. Biochemistry 48: 10342-10352. 19807072
Ladenburger, E.M. and H. Plattner. (2011). Calcium-release channels in paramecium. Genomic expansion, differential positioning and partial transcriptional elimination. PLoS One 6: e27111. 22102876
Ladenburger, E.M., I. Korn, N. Kasielke, T. Wassmer, and H. Plattner. (2006). An Ins(1,4,5)P3 receptor in Paramecium is associated with the osmoregulatory system. J Cell Sci 119: 3705-3717. 16912081
Ladenburger, E.M., I.M. Sehring, I. Korn, and H. Plattner. (2009). Novel types of Ca2+ release channels participate in the secretory cycle of Paramecium cells. Mol. Cell Biol. 29: 3605-3622. 19380481
Laver, D.R., T. Hamada, J.D. Fessenden, and N. Ikemoto. (2007). The ryanodine receptor pore blocker neomycin also inhibits channel activity via a previously undescribed high-affinity Ca2+ binding site. J. Membr. Biol. 220: 11-20. 17879109
Lee, A.G. (1996). The ryanodine receptor. In: Biomembranes, Vol. 6, Transmembrane Receptors and Channels (A.G. Lee, ed.), JAI Press, Denver, CO., pp. 291-326.
Lur, G., M.W. Sherwood, E. Ebisui, L. Haynes, S. Feske, R. Sutton, R.D. Burgoyne, K. Mikoshiba, O.H. Petersen, and A.V. Tepikin. (2011). InsP₃receptors and Orai channels in pancreatic acinar cells: co-localization and its consequences. Biochem. J. 436: 231-239. 21568942
Meng, X., G. Wang, C. Viero, Q. Wang, W. Mi, X.D. Su, T. Wagenknecht, A.J. Williams, Z. Liu, and C.C. Yin. (2009). CLIC2-RyR1 interaction and structural characterization by cryo-electron microscopy. J. Mol. Biol. 387: 320-334. 19356589
Michikawa, T., H. Hamanake, H. Otsu, A. Yamamoto, A. Miyawaki, T. Furuichi, Y. Tashiro and K. Mikoshiba (1994). Transmembrane topology and sites of N-glycosylation of inositol 1,4,5-triphosphate receptor. J. Biol. Chem. 269: 9184-9189. 8132655
Mikoshiba, K. (2012). The Discovery and Structural Investigation of the IP(3) Receptor and the Associated IRBIT Protein. Adv Exp Med Biol 740: 281-304. 22453947
Mikoshiba, K., T. Furuichi, and A. Miyawaki (1996). IP3-sensitive calcium channel. J. Biochem. Biomem. 6: 273-289.
Plattner, H., I.M. Sehring, I.K. Mohamed, K. Miranda, W. De Souza, R. Billington, A. Genazzani, and E.M. Ladenburger. (2012). Calcium signaling in closely related protozoan groups (Alveolata): non-parasitic ciliates (Paramecium, Tetrahymena) vs. parasitic Apicomplexa (Plasmodium, Toxoplasma). Cell Calcium 51: 351-382. 22387010
Saier, M.H., Jr., B.H. Eng, S. Fard, J. Garg, D.A. Haggerty, W.J. Hutchinson, D.L. Jack, E.C. Lai, H.J. Liu, D.P. Nusinew, A.M. Omar, S.S. Pao, I.T. Paulsen, J.A. Quan, M. Sliwinski, T.-T. Tseng, S. Wachi and G.B. Young (1999). Phylogenetic characterization of novel transport protein families revealed by genome analyses. Biochem. Biophys. Acta 1422: 1-56. 10082980
Schug, Z.T., P.C. da Fonseca, C.D. Bhanumathy, L. Wagner, 2nd, X. Zhang, B. Bailey, E.P. Morris, D.I. Yule, and S.K. Joseph. (2008). Molecular characterization of the inositol 1,4,5-trisphosphate receptor pore-forming segment. J. Biol. Chem. 283: 2939-2948. 18025085
Seo, M.D., S. Velamakanni, N. Ishiyama, P.B. Stathopulos, A.M. Rossi, S.A. Khan, P. Dale, C. Li, J.B. Ames, M. Ikura, and C.W. Taylor. (2012). Structural and functional conservation of key domains in InsP3 and ryanodine receptors. Nature 483: 108-112. 22286060
Subedi, K.P., T.D. Singh, J.C. Kim, and S.H. Woo. (2012). Cloning and expression of a new inositol 1,4,5-trisphosphate receptor type 1 splice variant in adult rat atrial myocytes. Cell Mol Biol Lett 17: 124-135. 22207335
Sun, Q.A., D.T. Hess, L. Nogueira, S. Yong, D.E. Bowles, J. Eu, K.R. Laurita, G. Meissner, and J.S. Stamler. (2011). Oxygen-coupled redox regulation of the skeletal muscle ryanodine receptor-Ca2+ release channel by NADPH oxidase 4. Proc. Natl. Acad. Sci. USA 108: 16098-16103. 21896730
Thomas, N.L., C.H. George, A.J. Williams, and F.A. Lai. (2007). Ryanodine receptor mutations in arrhythmias: advances in understanding the mechanisms of channel dysfunction. Biochem. Soc. Trans. 35:946-951. 17956252
Tunwell, R.E.A., C. Wickenden, B.M.A. Bertrand, V.I. Shevchenko, M.B. Walsh, P.D. Allen and F.A. Lai (1996). The human cardiac muscle ryanodine receptor-calcium release channel: identification, primary structure and topological analysis. Biochem. J. 318: 477-487. 8809036
Van Petegem, F. (2012). Ryanodine receptors: structure and function. J. Biol. Chem. 287: 31624-31632. 22822064
Wu, S., F. Wang, J. Huang, Q. Fang, Z. Shen, and G. Ye. (2013). Molecular and cellular analyses of a ryanodine receptor from hemocytes of Pieris rapae. Dev Comp Immunol 41: 1-10. 23603125
Xia, R., T. Stangler and J.J. Abramson (2000). Skeletal muscle ryanodine receptor is a redox sensor with a well defined redox potential that is sensitive to channel modulators. J. Biol. Chem. 275: 36556-36561. 10952995
Xu, L., Y. Wang, N. Yamaguchi, D.A. Pasek, and G. Meissner. (2008). Single channel properties of heterotetrameric mutant RyR1 ion channels linked to core myopathies. J. Biol. Chem. 283: 6321-6329. 18171678
Zhao, M., P. Li, X. Li, L. Zhang, R.J. Winkfein and S.R.W. Chen (1999). Molecular identification of the ryanodine receptor pore-forming segment. J. Biol. Chem. 274: 25971-25974. 10473538