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Márquez-Moñino MÁ, Ortega-García R, Whitfield H, Riley AM, Infantes L, Garrett SW, Shipton ML, Brearley CA, Potter BVL, González B. Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity. Nat Commun 2024; 15:1502. [PMID: 38374076 PMCID: PMC10876669 DOI: 10.1038/s41467-024-45917-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 02/05/2024] [Indexed: 02/21/2024] Open
Abstract
D-myo-inositol 1,4,5-trisphosphate (InsP3) is a fundamental second messenger in cellular Ca2+ mobilization. InsP3 3-kinase, a highly specific enzyme binding InsP3 in just one mode, phosphorylates InsP3 specifically at its secondary 3-hydroxyl group to generate a tetrakisphosphate. Using a chemical biology approach with both synthetised and established ligands, combining synthesis, crystallography, computational docking, HPLC and fluorescence polarization binding assays using fluorescently-tagged InsP3, we have surveyed the limits of InsP3 3-kinase ligand specificity and uncovered surprisingly unforeseen biosynthetic capacity. Structurally-modified ligands exploit active site plasticity generating a helix-tilt. These facilitated uncovering of unexpected substrates phosphorylated at a surrogate extended primary hydroxyl at the inositol pseudo 3-position, applicable even to carbohydrate-based substrates. Crystallization experiments designed to allow reactions to proceed in situ facilitated unequivocal characterization of the atypical tetrakisphosphate products. In summary, we define features of InsP3 3-kinase plasticity and substrate tolerance that may be more widely exploitable.
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Affiliation(s)
- María Ángeles Márquez-Moñino
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain
| | - Raquel Ortega-García
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain
| | - Hayley Whitfield
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew M Riley
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Lourdes Infantes
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain
| | - Shane W Garrett
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Megan L Shipton
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Charles A Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Barry V L Potter
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - Beatriz González
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain.
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2
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Shipton ML, Riley AM, Rossi AM, Brearley CA, Taylor CW, Potter BVL. Both d- and l-Glucose Polyphosphates Mimic d- myo-Inositol 1,4,5-Trisphosphate: New Synthetic Agonists and Partial Agonists at the Ins(1,4,5)P 3 Receptor. J Med Chem 2020; 63:5442-5457. [PMID: 32286062 PMCID: PMC7260056 DOI: 10.1021/acs.jmedchem.0c00215] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Chiral sugar derivatives are potential
cyclitol surrogates of the
Ca2+-mobilizing intracellular messenger d-myo-inositol 1,4,5-trisphosphate [Ins(1,4,5)P3]. Six novel polyphosphorylated analogues derived from both d- and l-glucose were synthesized. Binding to Ins(1,4,5)P3 receptors [Ins(1,4,5)P3R] and the ability to release
Ca2+ from intracellular stores via type 1 Ins(1,4,5)P3Rs were investigated. β-d-Glucopyranosyl 1,3,4-tris-phosphate,
with similar phosphate regiochemistry and stereochemistry to Ins(1,4,5)P3, and α-d-glucopyranosyl 1,3,4-tris-phosphate
are full agonists, being equipotent and 23-fold less potent than Ins(1,4,5)P3, respectively, in Ca2+-release assays and similar
to Ins(1,4,5)P3 and 15-fold weaker in binding assays. They
can be viewed as truncated analogues of adenophostin A and refine
understanding of structure-activity relationships for this Ins(1,4,5)P3R agonist. l-Glucose-derived ligands, methyl α-l-glucopyranoside 2,3,6-trisphosphate and methyl α-l-glucopyranoside 2,4,6-trisphosphate, are also active, while
their corresponding d-enantiomers, methyl α-d-glucopyranoside 2,3,6-trisphosphate and methyl α-d-glucopyranoside 2,4,6-trisphosphate, are inactive. Interestingly,
both l-glucose-derived ligands are partial agonists: they
are among the least efficacious agonists of Ins(1,4,5)P3R yet identified, providing new leads for antagonist development.
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Affiliation(s)
- Megan L Shipton
- Drug Discovery & Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U. K
| | - Andrew M Riley
- Drug Discovery & Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U. K
| | - Ana M Rossi
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U. K
| | - Charles A Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U. K
| | - Colin W Taylor
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U. K
| | - Barry V L Potter
- Drug Discovery & Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U. K
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3
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Duchek J, Adams DR, Hudlicky T. Chemoenzymatic Synthesis of Inositols, Conduritols, and Cyclitol Analogues. Chem Rev 2011; 111:4223-58. [DOI: 10.1021/cr1004138] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Duchek
- Department of Chemistry and the Centre for Biotechnology, Brock University, 500 Glenridge Avenue, St. Catharines ON L2S 3A1, Canada
| | - David R. Adams
- Department of Chemistry and the Centre for Biotechnology, Brock University, 500 Glenridge Avenue, St. Catharines ON L2S 3A1, Canada
| | - Tomas Hudlicky
- Department of Chemistry and the Centre for Biotechnology, Brock University, 500 Glenridge Avenue, St. Catharines ON L2S 3A1, Canada
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4
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Sureshan KM, Devaraj S, Shashidhar MS. Regioselective O-acylation of myo-inositol 1,3,5-orthoesters: dependence of regioselectivity on the stoichiometry of the base. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.01.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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5
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Masayama A, Takahashi T, Tsukada K, Nishikawa S, Takahashi R, Adachi M, Koga K, Suzuki A, Yamane T, Nakano H, Iwasaki Y. Streptomyces Phospholipase D Mutants with Altered Substrate Specificity Capable of Phosphatidylinositol Synthesis. Chembiochem 2008; 9:974-81. [DOI: 10.1002/cbic.200700528] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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6
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Riggs BM, Lansley TA, Ryals PE. Phosphatidylinositol synthase of Tetrahymena: inositol isomers as substrates in phosphatidylinositol biosynthesis and headgroup exchange reactions. J Eukaryot Microbiol 2007; 54:119-24. [PMID: 17403152 DOI: 10.1111/j.1550-7408.2007.00242.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphatidylinositol (PtdIns) synthase in microsomal fractions derived from Tetrahymena vorax was studied to determine its activity requirements. The suitability of inositol isomers as substrates for the synthase and in headgroup exchange reactions also was investigated. Tetrahymena PtdIn synthase activity was optimum in the presence of 2 mM MgCl2 plus 2 mM MnCl2, a pH of 7.8, and a temperature of 30 degrees C. The enzyme retained approximately 80% of its activity after incubation at 70 degrees C for 10 min. PtdIns headgroup exchange activity was maximal in the presence of cytidine monophosphate. By following either the accumulation of radiolabeled reaction products or the loss of radiolabel from precursors, each of the inositol isomers tested appeared to serve as substrates for both the PtdIns synthase and PtdIns:inositol phosphatidyl transferase activities. In each case, myo-inositol and scyllo-inositol were the preferred substrates. The data suggest two routes for the formation of phosphatidyl-non-myo-inositols in Tetrahymena and the potential for the production of novel, non-myo-inositol-containing second messengers.
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Affiliation(s)
- Bridget M Riggs
- Department of Biology, The University of West Florida, Pensacola, Florida 32514, USA
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7
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Hans S, Mootoo DR. A de novo approach to C-branched inositols: synthesis of a myo-inositol precursor for C-linked glycosyl phosphatidylinositols. Carbohydr Res 2006; 341:1322-32. [PMID: 16698000 DOI: 10.1016/j.carres.2006.04.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Revised: 04/16/2006] [Accepted: 04/18/2006] [Indexed: 10/24/2022]
Abstract
C-Linked glycosyl inositols are valuable structure-activity probes because of their greater hydrolytic stability and different conformational behavior compared with their parent O-glycosides. Simple C-branched inositols are synthetic precursors to these and other groups of inositol mimetics. Herein is described a de novo synthesis of C-branched inositols that contain a versatile ethenyl side chain for elaboration into more complex appendages. The approach centers on a stereoselective oxocarbenium ion-allylsilane cyclization and provides C-branched inositols with different stereochemical motifs. The synthesis of C-ethenyl-di-O-isopropylidene-myo-, neo-, epi-, and allo-inositols is discussed.
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Affiliation(s)
- Sunej Hans
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10021, USA
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8
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Chelation controlled regiospecific O-substitution of myo-inositol orthoesters: convenient access to orthogonally protected myo-inositol derivatives. Tetrahedron 2005. [DOI: 10.1016/j.tet.2004.11.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Soengas RG, Estévez JC, Estévez RJ. Transformation of D-glucose into 1D-3-deoxy-3-hydroxymethyl-myo-inositol by stereocontrolled intramolecular Henry reaction. Org Lett 2004; 5:4457-9. [PMID: 14602024 DOI: 10.1021/ol035771x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] An intramolecular Henry cyclization provides a promising new strategy for the transformation of nitroheptofuranoses into deoxyhydroxymethylinositols. This method has allowed a stereospecific transformation of d-glucose into 1D-3-deoxy-3-hydroxymethyl-myo-inositol.
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Affiliation(s)
- Raquel G Soengas
- Departamento de Química Orgánica, Universidade de Santiago, 15782 Santiago de Compostela, Spain
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10
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Sureshan KM, Watanabe Y. An efficient route to optically active inositol derivatives via the resolution of myo-inositol 1,3,5-orthoformate: a short synthesis of d-myo-inositol-4-phosphate. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2004.02.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Sureshan KM, Shashidhar MS, Praveen T, Das T. Regioselective Protection and Deprotection of Inositol Hydroxyl Groups. Chem Rev 2003; 103:4477-503. [PMID: 14611268 DOI: 10.1021/cr0200724] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kana M Sureshan
- Division of Organic Synthesis, National Chemical Laboratory, Pune 411 008, India
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12
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Sureshan KM, Shashidhar MS, Praveen T, Gonnade RG, Bhadbhade MM. Sulfonate protecting groups. Regioselective sulfonylation of myo-inositol orthoesters-improved synthesis of precursors of D- and L-myo-inositol 1,3,4,5-tetrakisphosphate, myo-inositol 1,3,4,5,6-pentakisphosphate and related derivatives. Carbohydr Res 2002; 337:2399-410. [PMID: 12493224 DOI: 10.1016/s0008-6215(02)00298-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The regioselectivity of sulfonylation of myo-inositol orthoesters was controlled by the use of different bases to obtain the desired sulfonate. Monosulfonylation of myo-inositol orthoesters in the presence of one equivalent of sodium hydride or triethylamine resulted in the sulfonylation of the 4-hydroxyl group. The use of pyridine as a base for the same reaction resulted in sulfonylation of the 2-hydroxyl group. Disulfonylation of these orthoesters in the presence of excess sodium hydride yielded the 4,6-di-O-sulfonylated orthoesters. However, the use of triethylamine or pyridine instead of sodium hydride yielded the 2,4-di-O-sulfonylated orthoester. Sulfonylated derivatives of myo-inositol orthoesters were stable to conditions of O-alkylation but were cleaved using magnesium/methanol or sodium methoxide in methanol to regenerate the corresponding myo-inositol orthoester derivative. These new methods of protection-deprotection have been used: (i) for the efficient synthesis of enantiomers of 2,4-di-O-benzyl-myo-inositol, which are precursors for the synthesis of D- and L-myo-inositol 1,3,4,5-tetrakisphosphate; (ii) for the preparation of 2-O-benzyl-myo-inositol which is a precursor for the preparation of myo-inositol 1,3,4,5,6-pentakisphosphate.
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Affiliation(s)
- Kana M Sureshan
- Division of Organic Synthesis, National Chemical Laboratory, Pune 411 008, India
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13
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Hotoda H, Murayama K, Miyamoto S, Iwata Y, Takahashi M, Kawase Y, Tanzawa K, Kaneko M. Molecular recognition of adenophostin, a very potent Ca2+ inducer, at the D-myo-inositol 1,4,5-trisphosphate receptor. Biochemistry 1999; 38:9234-41. [PMID: 10413497 DOI: 10.1021/bi990114r] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recognition mode of adenophostin A at the D-myo-inositol 1,4, 5-trisphosphate [Ins(1,4,5)P(3)] receptor was investigated. Comparison of conformations of Ins(1,4,5)P(3) and adenophostin A by using the combination of NMR and molecular mechanics (MM) calculations demonstrated that adenophostin A adopted a moderately extended conformation regarding the distance between the 2'-phosphoryl group and the 3' ',4' '-bisphosphate motif, as suggested previously [Wilcox, R. A. et al. (1995) Mol. Pharmacol. 47, 1204-1211]. Based on the nuclear Overhauser effect (NOE) observed between 3'-H and 1' '-H and on MM calculations, the molecular shape of adenophostin A proved to be an extended form at least in solution, in contrast to Wilcox's compactly folded, preliminary hairpin model. GlcdR(2,3',4')P(3), an adenophostin analogue without adenine moiety, was found to be less potent than adenophostin A and almost equipotent to Ins(1,4,5)P(3). We propose the possibility that (i) the optimal spatial arrangement of the three phosphoryl groups and/or (ii) the interaction of the adenine moiety of adenophostin A with the putative binding site, if it exists in the vicinity of the Ins(1,4,5)P(3)-binding site, might account for the exceptional potency of adenophostin A.
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MESH Headings
- Adenosine/analogs & derivatives
- Adenosine/chemical synthesis
- Adenosine/chemistry
- Adenosine/metabolism
- Animals
- Binding Sites
- Calcium/metabolism
- Calcium Channels/chemistry
- Calcium Channels/metabolism
- Cerebellum/metabolism
- Glucosides/metabolism
- Inositol 1,4,5-Trisphosphate/agonists
- Inositol 1,4,5-Trisphosphate/chemistry
- Inositol 1,4,5-Trisphosphate/metabolism
- Inositol 1,4,5-Trisphosphate Receptors
- Microsomes/metabolism
- Models, Molecular
- Nuclear Magnetic Resonance, Biomolecular
- Nucleic Acid Conformation
- Penicillium/chemistry
- Rats
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/metabolism
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Affiliation(s)
- H Hotoda
- Exploratory Chemistry Research and Biological Research Laboratories, Sankyo Co., Ltd., Tokyo, Japan.
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14
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Riley AM, Guédat P, Schlewer G, Spiess B, Potter BVL. A Conformationally Restricted Cyclic Phosphate Analogue of Inositol Trisphosphate: Synthesis and Physicochemical Properties. J Org Chem 1998. [DOI: 10.1021/jo9714425] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew M. Riley
- Department of Medicinal Chemistry, School of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K., and Laboratoire de Pharmacochimie Moléculaire, Faculté de Pharmacie, Universite Louis Pasteur, Strasbourg, France
| | - Philippe Guédat
- Department of Medicinal Chemistry, School of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K., and Laboratoire de Pharmacochimie Moléculaire, Faculté de Pharmacie, Universite Louis Pasteur, Strasbourg, France
| | - Gilbert Schlewer
- Department of Medicinal Chemistry, School of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K., and Laboratoire de Pharmacochimie Moléculaire, Faculté de Pharmacie, Universite Louis Pasteur, Strasbourg, France
| | - Bernard Spiess
- Department of Medicinal Chemistry, School of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K., and Laboratoire de Pharmacochimie Moléculaire, Faculté de Pharmacie, Universite Louis Pasteur, Strasbourg, France
| | - Barry V. L. Potter
- Department of Medicinal Chemistry, School of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K., and Laboratoire de Pharmacochimie Moléculaire, Faculté de Pharmacie, Universite Louis Pasteur, Strasbourg, France
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15
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Abstract
The inositol 1,4,5-trisphosphate receptor (InsP3R) is a ligand-gated Ca2+-release channel on intracellular Ca2+ store sites (such as the endoplasmic reticulum), and plays an important role in intracellular Ca2+ signaling in a wide variety of cell types. Recent studies have shown that binding of inositol 1,4,5-trisphosphate (InsP3) to InsP3R isoforms is differentially regulated by Ca2+, and that InsP3R functions are finely regulated by phosphorylation via tyrosine kinases and protein kinase C, by dephosphorylation via calcineurin, and by binding to FKBP (FK506-binding protein). In addition, transient receptor potential (TRP) and TRP-like proteins appear to couple conformationally with the InsP3R for capacitative Ca2+ entry. The importance of InsP3R signaling in neuronal function has been demonstrated by gene targeting in mice and by studies of T-cell receptor signaling, apoptosis, meiotic maturation, and cytokinesis.
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Affiliation(s)
- K Mikoshiba
- Department of Molecular Neurobiology, Institute of Medical Science University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108, Japan
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