Calcineurin

Crystallographic structure of calcineurin heterodimer composed of the catalytic (PPP3CA) and regulatory (PPP3R1) subunits.

Calcineurin (CaN) is a calcium and calmodulin dependent serine/threonine protein phosphatase (also known as protein phosphatase 3, and calcium-dependent serine-threonine phosphatase). ^[2] It activates the T cells of the immune system and can be blocked by drugs. Calcineurin activates nuclear factor of activated T cell cytoplasmic (NFATc), a transcription factor, by dephosphorylating it. The activated NFATc is then translocated into the nucleus, where it upregulates the expression of interleukin 2 (IL-2), which, in turn, stimulates the growth and differentiation of the T cell response. Calcineurin is the target of a class of drugs called calcineurin inhibitors, which include ciclosporin, voclosporin, pimecrolimus and tacrolimus.

Calcineurin is a highly conserved protein within eukaryotic life, appearing within organisms from yeasts to mammals. ^[3]

Structure

Calcineurin is a heterodimer of a 61-kD calmodulin-binding catalytic subunit, calcineurin A and a 19-kD Ca²⁺-binding regulatory subunit, calcineurin B. In humans, there are three isozymes of the catalytic subunit, each encoded by a separate gene (PPP3CA, PPP3CB, and PPP3CC) and two isoforms of the regulatory, also encoded by separate genes (PPP3R1, PPP3R2).

protein phosphatase 3, catalytic subunit, alpha isozyme Identifiers Symbol PPP3CA Alt. symbols CALN, CALNA NCBI gene 5530 HGNC 9314 OMIM 114105 RefSeq NM_000944 UniProt Q08209 Other data EC number 3.1.3.16 Locus Chr. 4 q24 Search for Structures Swiss-model Domains InterPro

protein phosphatase 3, catalytic subunit, beta isozyme Identifiers Symbol PPP3CB Alt. symbols CALNB NCBI gene 5532 HGNC 9315 OMIM 114106 RefSeq NM_021132 UniProt P16298 Other data EC number 3.1.3.16 Locus Chr. 10 q22.2 Search for Structures Swiss-model Domains InterPro

protein phosphatase 3, catalytic subunit, gamma isozyme Identifiers Symbol PPP3CC NCBI gene 5533 HGNC 9316 OMIM 114107 RefSeq NM_005605 UniProt P48454 Other data EC number 3.1.3.16 Locus Chr. 8 p21.3 Search for Structures Swiss-model Domains InterPro

protein phosphatase 3, regulatory subunit B, alpha Identifiers Symbol PPP3R1 NCBI gene 5534 HGNC 9317 OMIM 601302 RefSeq NM_000945 UniProt P63098 Other data EC number 3.1.3.16 Locus Chr. 2 p14 Search for Structures Swiss-model Domains InterPro

protein phosphatase 3, regulatory subunit B, beta Identifiers Symbol PPP3R2 NCBI gene 5535 HGNC 9318 OMIM 613821 RefSeq NM_147180 UniProt Q96LZ3 Other data EC number 3.1.3.16 Locus Chr. 9 q31 Search for Structures Swiss-model Domains InterPro

Calcineurin A contains the active site, which is between 57-9 kDa depending on isoform, with larger catalytic subunits found in lower eukaryotes such as Saccharomyces fungus ^[3] . This catalytic subunit consists of a catalytic domain homologous to other serine/threonine protein phosphatases as well as three unique regulatory domains at the COOH terminus ^[3] . These three regulatory domains were found to be the binding domain of the regulatory subunit of calcineurin B, the domain for calmodulin binding, and the autoinhibitory domain ^[3] . When calmodulin or Ca²⁺ is absent, the autoinhibitory domain binds to the active site, inhibiting activity ^[3] . Conformational changes with the binding of calmodulin or Ca²⁺ frees the active site and resumes calcineurin function ^[3] .

Mechanism of action

When an antigen-presenting cell interacts with a T cell receptor on T cells, there is an increase in the cytoplasmic level of calcium, which activates calcineurin by binding a regulatory subunit and activating calmodulin binding. ^[4] Calcineurin induces transcription factors (NFATs) that are important in the transcription of IL-2 genes. IL-2 activates T-helper lymphocytes and induces the production of other cytokines. In this way, it governs the action of cytotoxic lymphocytes. The amount of IL-2 being produced by the T-helper cells is believed to influence the extent of the immune response significantly.

Calcineurin directly dephosphorylates cytoplasmic subunits of the NFAT1 transcription complex, operating through direct binding through a conserved N terminus ^[5] . Translocation of the NFAT transcription factors into the nucleus is maintained via the concentration of Ca²⁺ ions due to the integration of Ca²⁺ signaling within mitogen-activated protein kinase in NFAT, the activity of Calmodulin can act as a coincidence detector for Ras signaling pathways ^[5] . Dissociation of histone deacetylase 4 (HDAC) by calcineurin leads to regulation of the Mef2 transcription factor, which mediates transition of fast muscle fibers to slow muscle fibers ^[5] . This ability to regulate muscular fiber conversion has implications for the developmental impact of the protein and also is believed to be connected to regulation of programmed cell death ^[5] .

Function

Formation of Structures in Newborn Mammals

Synaptic Connection

Calcineurin is suggested to be a critical component in the formation of synaptic connections. NFATc4 is found to be expressed in hippocampal neurons, with translocation via depolarization and normal synaptic activity ^[5] . This in conjunction with a potential downstream gene encoding a Ca²⁺ channel (IP3R1) form the basis for the potential linkage of calcineurin to synaptic connections, especially within newborn animals which have activation of IP3R1 ^[5] . Should further research support the possible connection between this protein and synapse connection, it would open new directions of study for neurological development in animals.

Cardiovascular

Heart valve formation and myocardial hypertrophy are also believed to be signaled through the calcineurin signaling pathway. Mutations in the NFATc1 gene are reported to cause failure of development in heart valves ^[5] , meaning that the calcineurin transcription factor controls a vital developmental pathway for survival of newborn animals. In transgenic mice presenting this mutation are shown to die from congestive heart failure in utero ^[3] . Stress-induced hypertrophy, a response in cardiac muscle cells, is dependent on calcium, and was discovered to also be induced by overexpression of calcineurin A ^[5] . Additionally, overexpression of NFATc4 could also induce similar results, and cyclosporin A prevents cardiac hypertrophy development in response to certain stimuli ^[5] .

Calcineurin is also found to play a critical role in the development of several other structures and functions, such as the liver, skin, inflammatory and immune response ^[5] . This is shown through the augmentation of suboptimal stimuli through the use of calcium, as well as blocking by cyclosporin A ^[5] .

Cell Cycle Arrest Recovery in Saccharomyces cerevisiae

Mediation of pheromone-induced growth arrest for mating is performed by a Ca²⁺ increase and activation of calcineurin ^[3] . Strains lacking in either of two yeast calcineurin A subunits were unable to recover from growth arrest ^[3] . Calmodulin is also found to be required from this growth arrest ^[3] , meaning that all factors which govern calcineurin activation as well as the protein itself are necessary for proper function of yeast cells. Without the ability to escape growth arrest, yeast cells are unable to exit G1, removing the ability to continue through the cell cycle and engage in asexual reproduction.

Functions in Sleep

Presence and abundance of Calcineurin Aα in mice affects the intensity of non-rapid eye movement sleep (NREMS) ^[6] . In mice which overexpression of the protein subunit occurs, it is observed that the amount of sleep and as a result wakefulness is increased ^[6] . Furthermore, deficiency or knockout of the subunit leads to diminished NREMS in affected mice ^[6] , showing the coupling of sleep with the function of the calcineurin protein. Severe insomnia was also exhibited in mice which lacked CnB1, as well as an increased circadian period as compared to wild type mice ^[6] .

Clinical relevance

Rheumatic diseases

Calcineurin inhibitors are prescribed for adult rheumatoid arthritis (RA) as a single drug or in combination with methotrexate. The microemulsion formulation is approved by the U.S. Food and Drug Administration for treatment of severely active RA. It is also prescribed for: psoriatic arthritis, psoriasis, acute ocular Behçet's disease, juvenile idiopathic arthritis, adult and juvenile polymyositis and dermatomyositis, adult and juvenile systemic lupus erythematosus, adult lupus membranous nephritis, systemic sclerosis, aplastic anemia, steroid-resistant nephrotic syndrome, atopic dermatitis, severe corticosteroid-dependent asthma, severe ulcerative colitis, pemphigus vulgaris, myasthenia gravis, and dry eye disease, with or without Sjögren's syndrome (administered as ophthalmic emulsion). ^[7]

Schizophrenia

Calcineurin is linked to receptors for several brain chemicals including glutamate, dopamine and GABA. ^[8] An experiment with genetically-altered mice that could not produce calcineurin showed similar symptoms as in humans with schizophrenia: impairment in working memory, attention deficits, aberrant social behavior, and several other abnormalities characteristic of schizophrenia. ^[9]

Diabetes

Calcineurin along with NFAT, may improve the function of diabetics' pancreatic beta cells. ^{[10] [11]} Thus tacrolimus contributes to the frequent development of new diabetes following renal transplantation. ^[12]

Calcineurin/NFAT signaling is required for perinatal lung maturation and function. ^[13]

Organ transplantation

Calcineurin inhibitors such as tacrolimus and ciclosporin are used to suppress the immune system in organ allotransplant recipients to prevent rejection of the transplanted tissue. ^[14]

Interactions

Calcineurin has been shown to interact with RCAN1 ^[15] and AKAP5. ^[16]

Viral Inhibition

Inhibition of calcineurin is also found to be performed by encoded proteins in viruses. Notably, the African swine fever virus encodes the A238L protein, which binds to calcineurin and inhibits translocation and function of NFATc ^[5] . Given sequence similarity between A238L and NFATc family members suggests that the protein induces cyclosporin-like immunosuppression in host cells ^[5] .

References

1. PDB: 1AUI ​; Kissinger CR, Parge HE, Knighton DR, Lewis CT, Pelletier LA, Tempczyk A, Kalish VJ, Tucker KD, Showalter RE, Moomaw EW (December 1995). "Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex". Nature. 378 (6557): 641–4. Bibcode:1995Natur.378..641K. doi:10.1038/378641a0. PMID   8524402. S2CID   4337105.
2. Liu L, Zhang J, Yuan J, Dang Y, Yang C, Chen X, Xu J, Yu L (March 2005). "Characterization of a human regulatory subunit of protein phosphatase 3 gene (PPP3RL) expressed specifically in testis". Mol. Biol. Rep. 32 (1): 41–5. doi:10.1007/s11033-004-4250-4. PMID   15865209. S2CID   43848098.
3. Rusnak, Frank; Mertz, Pamela (2000-01-10). "Calcineurin: Form and Function". Physiological Reviews. 80 (4): 1483–1521. doi:10.1152/physrev.2000.80.4.1483. ISSN   0031-9333. PMID   11015619.
4. Yamashita M, Katsumata M, Iwashima M, Kimura M, Shimizu C, Kamata T, Shin T, Seki N, Suzuki S, Taniguchi M, Nakayama T (June 2000). "T cell receptor-induced calcineurin activation regulates T helper type 2 cell development by modifying the interleukin 4 receptor signaling complex". J. Exp. Med. 191 (11): 1869–79. doi:10.1084/jem.191.11.1869. PMC   2213529 . PMID   10839803.
5. Crabtree, Gerald R. (January 2001). "Calcium, Calcineurin, and the Control of Transcription". Journal of Biological Chemistry. 276 (4): 2313–2316. doi: 10.1074/jbc.R000024200 . PMID   11096121.
6. Yin, Xin; Zhang, Zihan; Zhou, Rui; Zuo, Peng; Sang, Di; Zhou, Shuang; Shi, Bihan; Chen, Lin; Wu, Chongyang; Guo, Ying; Wang, Fengchao; Zhang, Eric Erquan; Li, Qi; Yanagisawa, Masashi; Liu, Qinghua (2025-01-28). "Calcineurin governs baseline and homeostatic regulations of non–rapid eye movement sleep in mice". Proceedings of the National Academy of Sciences. 122 (4) e2418317122. doi:10.1073/pnas.2418317122. ISSN   0027-8424. PMC   11789068 . PMID   39847332.
7. "Pharmacology and side effects of cyclosporine and tacrolimus". UpToDate. 2014-04-10.
8. Bannai H, Lévi S, Schweizer C, Inoue T, Launey T, Racine V, Sibarita JB, Mikoshiba K, Triller A (2009). "Activity-dependent tuning of inhibitory neurotransmission based on GABAAR diffusion dynamics". Neuron. 62 (5): 670–82. doi: 10.1016/j.neuron.2009.04.023 . PMID   19524526. S2CID   18512241.
9. Miyakawa T, Leiter LM, Gerber DJ, Gainetdinov RR, Sotnikova TD, Zeng H, Caron MG, Tonegawa S (July 2003). "Conditional calcineurin knockout mice exhibit multiple abnormal behaviors related to schizophrenia". Proc. Natl. Acad. Sci. U.S.A. 100 (15): 8987–92. Bibcode:2003PNAS..100.8987M. doi: 10.1073/pnas.1432926100 . PMC   166425 . PMID   12851457.
10. Heit JJ, Apelqvist AA, Gu X, Winslow MM, Neilson JR, Crabtree GR, Kim SK (September 2006). "Calcineurin/NFAT signalling regulates pancreatic beta-cell growth and function". Nature. 443 (7109): 345–9. Bibcode:2006Natur.443..345H. doi:10.1038/nature05097. PMID   16988714. S2CID   4397036.
11. Heit JJ (October 2007). "Calcineurin/NFAT signaling in the beta-cell: From diabetes to new therapeutics". BioEssays. 29 (10): 1011–21. doi:10.1002/bies.20644. PMID   17876792. S2CID   21027866.
12. Crutchlow MF, Bloom RD (2007). "Transplant-associated hyperglycemia: a new look at an old problem". Clin J Am Soc Nephrol. 2 (2): 343–55. doi: 10.2215/CJN.03671106 . PMID   17699434.
13. Davé V, Childs T, Xu Y, Ikegami M, Besnard V, Maeda Y, Wert SE, Neilson JR, Crabtree GR, Whitsett JA (October 2006). "Calcineurin/Nfat signaling is required for perinatal lung maturation and function". J. Clin. Invest. 116 (10): 2597–609. doi:10.1172/JCI27331. PMC   1570374 . PMID   16998587.
14. "Tacrolimus". New Zealand Formulary v81. 1 March 2019.
15. Fuentes JJ, Genescà L, Kingsbury TJ, Cunningham KW, Pérez-Riba M, Estivill X, de la Luna S (July 2000). "DSCR1, overexpressed in Down syndrome, is an inhibitor of calcineurin-mediated signaling pathways". Hum. Mol. Genet. 9 (11): 1681–90. doi: 10.1093/hmg/9.11.1681 . PMID   10861295.
16. Kashishian A, Howard M, Loh C, Gallatin WM, Hoekstra MF, Lai Y (October 1998). "AKAP79 inhibits calcineurin through a site distinct from the immunophilin-binding region". J. Biol. Chem. 273 (42): 27412–9. doi: 10.1074/jbc.273.42.27412 . PMID   9765270.

Further reading

• Cottrell JR, Levenson JM, Kim SH, Gibson HE, Richardson KA, Sivula M, Li B, Ashford CJ, Heindl KA, Babcock RJ, Rose DM, Hempel CM, Wiig KA, Laeng P, Levin ME, Ryan TA, Gerber DJ (July 2013). "Working memory impairment in calcineurin knock-out mice is associated with alterations in synaptic vesicle cycling and disruption of high-frequency synaptic and network activity in prefrontal cortex". J. Neurosci. 33 (27): 10938–49. doi:10.1523/JNEUROSCI.5362-12.2013. PMC   3718364 . PMID   23825400.
• Crabtree GR (1999). "Generic signals and specific outcomes: signaling through Ca2+, calcineurin, and NF-AT". Cell. 96 (5): 611–4. doi: 10.1016/S0092-8674(00)80571-1 . PMID   10089876. S2CID   8817053.
• Giri PR, Higuchi S, Kincaid RL (1991). "Chromosomal mapping of the human genes for the calmodulin-dependent protein phosphatase (calcineurin) catalytic subunit". Biochem. Biophys. Res. Commun. 181 (1): 252–8. Bibcode:1991BBRC..181..252R. doi:10.1016/S0006-291X(05)81410-X. PMID   1659808.
• Kincaid RL, Giri PR, Higuchi S, Tamura J, Dixon SC, Marietta CA, Amorese DA, Martin BM (1990). "Cloning and characterization of molecular isoforms of the catalytic subunit of calcineurin using nonisotopic methods". J. Biol. Chem. 265 (19): 11312–9. doi: 10.1016/S0021-9258(19)38593-X . PMID   2162844.
• Guerini D, Klee CB (1989). "Cloning of human calcineurin A: evidence for two isozymes and identification of a polyproline structural domain". Proc. Natl. Acad. Sci. U.S.A. 86 (23): 9183–7. Bibcode:1989PNAS...86.9183G. doi: 10.1073/pnas.86.23.9183 . PMC   298458 . PMID   2556704.
• Kincaid RL, Nightingale MS, Martin BM (1988). "Characterization of a cDNA clone encoding the calmodulin-binding domain of mouse brain calcineurin". Proc. Natl. Acad. Sci. U.S.A. 85 (23): 8983–7. Bibcode:1988PNAS...85.8983K. doi: 10.1073/pnas.85.23.8983 . PMC   282646 . PMID   2848250.
• Coghlan VM, Perrino BA, Howard M, Langeberg LK, Hicks JB, Gallatin WM, Scott JD (1995). "Association of protein kinase A and protein phosphatase 2B with a common anchoring protein". Science. 267 (5194): 108–11. Bibcode:1995Sci...267..108C. doi:10.1126/science.7528941. PMID   7528941.
• Griffith JP, Kim JL, Kim EE, Sintchak MD, Thomson JA, Fitzgibbon MJ, Fleming MA, Caron PR, Hsiao K, Navia MA (1995). "X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex". Cell. 82 (3): 507–22. doi: 10.1016/0092-8674(95)90439-5 . PMID   7543369. S2CID   15502270.
• Shibasaki F, McKeon F (1995). "Calcineurin functions in Ca(2+)-activated cell death in mammalian cells". J. Cell Biol. 131 (3): 735–43. doi:10.1083/jcb.131.3.735. PMC   2120616 . PMID   7593193.
• Muramatsu T, Kincaid RL (1993). "Molecular cloning of a full-length cDNA encoding the catalytic subunit of human calmodulin-dependent protein phosphatase (calcineurin A alpha)". Biochim. Biophys. Acta. 1178 (1): 117–20. doi:10.1016/0167-4889(93)90117-8. PMID   8392375.
• Cameron AM, Steiner JP, Roskams AJ, Ali SM, Ronnett GV, Snyder SH (1995). "Calcineurin associated with the inositol 1,4,5-trisphosphate receptor-FKBP12 complex modulates Ca2+ flux". Cell. 83 (3): 463–72. doi: 10.1016/0092-8674(95)90124-8 . PMID   8521476. S2CID   11594556.
• Kissinger CR, Parge HE, Knighton DR, Lewis CT, Pelletier LA, Tempczyk A, Kalish VJ, Tucker KD, Showalter RE, Moomaw EW (1995). "Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex". Nature. 378 (6557): 641–4. Bibcode:1995Natur.378..641K. doi:10.1038/378641a0. PMID   8524402. S2CID   4337105.
• Wang MG, Yi H, Guerini D, Klee CB, McBride OW (1996). "Calcineurin A alpha (PPP3CA), calcineurin A beta (PPP3CB) and calcineurin B (PPP3R1) are located on human chromosomes 4, 10q21-->q22 and 2p16-->p15 respectively". Cytogenet. Cell Genet. 72 (2–3): 236–41. doi:10.1159/000134198. PMID   8978785.
• Shibasaki F, Kondo E, Akagi T, McKeon F (1997). "Suppression of signalling through transcription factor NF-AT by interactions between calcineurin and Bcl-2". Nature. 386 (6626): 728–31. Bibcode:1997Natur.386..728S. doi:10.1038/386728a0. PMID   9109491. S2CID   4277216.
• Kashishian A, Howard M, Loh C, Gallatin WM, Hoekstra MF, Lai Y (1998). "AKAP79 inhibits calcineurin through a site distinct from the immunophilin-binding region". J. Biol. Chem. 273 (42): 27412–9. doi: 10.1074/jbc.273.42.27412 . PMID   9765270.
• Wang HG, Pathan N, Ethell IM, Krajewski S, Yamaguchi Y, Shibasaki F, McKeon F, Bobo T, Franke TF, Reed JC (1999). "Ca2+-induced apoptosis through calcineurin dephosphorylation of BAD". Science. 284 (5412): 339–43. Bibcode:1999Sci...284..339W. doi:10.1126/science.284.5412.339. PMID   10195903.
• Fuentes JJ, Genescà L, Kingsbury TJ, Cunningham KW, Pérez-Riba M, Estivill X, de la Luna S (2000). "DSCR1, overexpressed in Down syndrome, is an inhibitor of calcineurin-mediated signaling pathways". Hum. Mol. Genet. 9 (11): 1681–90. doi: 10.1093/hmg/9.11.1681 . PMID   10861295.
• Hartley JL, Temple GF, Brasch MA (2000). "DNA cloning using in vitro site-specific recombination". Genome Res. 10 (11): 1788–95. doi:10.1101/gr.143000. PMC   310948 . PMID   11076863.
• Frey N, Richardson JA, Olson EN (2000). "Calsarcins, a novel family of sarcomeric calcineurin-binding proteins". Proc. Natl. Acad. Sci. U.S.A. 97 (26): 14632–7. Bibcode:2000PNAS...9714632F. doi: 10.1073/pnas.260501097 . PMC   18970 . PMID   11114196.
• Siddiq A, Miyazaki T, Takagishi Y, Kanou Y, Hayasaka S, Inouye M, Seo H, Murata Y (2001). "Expression of ZAKI-4 messenger ribonucleic acid in the brain during rat development and the effect of hypothyroidism". Endocrinology. 142 (5): 1752–9. doi: 10.1210/endo.142.5.8156 . PMID   11316738.

External links

• Calcineurin at the U.S. National Library of Medicine Medical Subject Headings (MeSH)