Phosphatase Subfamily PTPRN

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Phosphatase Classification: Fold CC1: Superfamily CC1: Family PTP: Subfamily PTPRN

PTPRN is a receptor lipid phosphatase family involved in secretion in neuronal and endocrine tissues, including insulin release.


PTPRN is found across metazoans, with no obvious losses. Human has two members, PTPRN (IA-2/ICA521) and PTPRN2 (phogrin/IA-2b).

Domain Structure

Human PTPRNs have a extracellular region containning an N-terminal RESP18 domain and a membrane-proximal a ferredoxin-like domain (also known as Receptor_IA-2) [1, 2, 3]. The RESP18 is vertebrate specific, and the ferredoxin-like domain is also lost in nematodes. Drosophila and some other insects lack a clear signal peptide. This may phenocopy the proteolytic cleavage of the cytoplasmic region seen in mammalian PTPRNs.

The cytoplasmic region has a putative PEST motif, followed by a phosphatase domain flanked by two short regions required to bind the β2‐syntrophin PDZ domain [4].


Human PTPRN and PTPRN2 are expressed in pancreatic beta cells and were first characterized as autoantigens leading to type I diabetes. They are also abundantly expressed in brain. They cycle between secretory vesicles and the plasma membrane and are believed to be involved in both endocrine and neuronal exocytosis [5].

Both proteins have alterations to key residues in the phosphatase domain and lack phosphatase activity against PNPP or protein substrates. Back mutation of D936A within the Cx5R motif of rat PTPRN2 restored some catalytic function against PNPP [6], and additional mutations to restore the Y of the KNRY motif, and the P and D of the WPD motif further increased PNPP activity in mouse PTPRN (H740Y/A877D/D911A) or PTPRN2 (S762Y/Y898P/D933A) [7]. Rat PTPRN2 has been reported to act as a phosphatidylinositol phosphatase [8], so these alterations to conserved motifs may play a role in substrate specificity rather than catalytic activity, and suggest that all family members may be phosphatidylinositol rather than protein phosphatases.


PTPRN, aka IA-2 or ICA512 (Islet cell antigen 512), was first isolated from an islet cDNA expression library by screening with human insulin-dependent diabetes mellitus sera [9]. It is an autoantigen of type I diabetes and an intrinsic membrane protein of neurosecretory granules [10, 11]. PTPRN was found in normal human brain, pituitary, pancreas, and brain tumor cell lines, but not in a variety of other normal or tumor tissues [12]. (note: the tissue expression is supported by RNA-seq data from GTEx project).

PTPRN associates with the secretory granules (SGs) of neuroendocrine cells including pancreatic beta-cells. The exocytosis of SGs and insertion of PTPRN in the plasma membrane promotes the calcium-dependent cleavage of PTPRN cytoplasmic domain by mu-calpain, a calcium-dependent, non-lysosomal cysteine proteases (proteolytic enzymes). The cleavage occurs at the plasma membrane and generates an PTPRN cytosolic fragment that is targeted to the nucleus, where it binds the E3-SUMO ligase protein inhibitor of activated signal transducer and activator of transcription-y (PIASy) and up-regulates insulin expression [13].

Meanwhile, PTPRN binds beta2-syntrophin, a modular adapter interacts with proteins in actin cytoskeleton (e.g. utrophin). The association is mediated by PTPRN cytoplasmic region (663-700) and beta2-syntrophin PDZ domain. In vitro mu-calpain cleaves PTPRN at the site within the region mediates PTPRN binding to beta2-syntrophin [4, 14].

Alternative splicing determines differential PTPRN expression in islets compared with thymus and spleen. Islets express full-length mRNA and two alternatively spliced transcripts, whereas thymus and spleen exclusively express an alternatively spliced transcript lacking exon 13. This difference in splicing may play a permissive role in the development of autoimmune responses to PTPRN [15].

PTPRN2 (IA-2beta/phogrin/ICAAR)

PTPRN2 (Phogrin) is an additional major autoantigen for type I diabetes [16]. In patients with type 1 diabetes, autoantibodies to IA-2beta appear years before the development of clinical disease []. PTPRN2 was found in human brain, pituitary and pancreas, but not or at very low level in a variety of other normal or tumor tissues [17] (also see GTEx). But, its immature isoform proPTPRN2 is overexpressed in various cancers, including breast cancer. High proPTPRN2 expression was associated strongly with lymph node-positive breast cancer and poor clinical outcome [18].

Drosophila IA-2

IA-2 modulates insulin-like peptide expression expression and is expressed in the central nervous system and midgut [19]. The neuronal expression pattern was very similar to that mammalian PTPRN.

C. elegans ida-1

ida-1 is involved in dense-core vesicle cargo release with parallels to insulin signaling in mammals [20, 21].

Technical notes


  1. Primo ME, Klinke S, Sica MP, Goldbaum FA, Jakoncic J, Poskus E, and Ermácora MR. Structure of the mature ectodomain of the human receptor-type protein-tyrosine phosphatase IA-2. J Biol Chem. 2008 Feb 22;283(8):4674-81. DOI:10.1074/jbc.M708144200 | PubMed ID:18048354 | HubMed [Primo08]
  2. Primo ME, Jakoncic J, Noguera ME, Risso VA, Sosa L, Sica MP, Solimena M, Poskus E, and Ermácora MR. Protein-protein interactions in crystals of the human receptor-type protein tyrosine phosphatase ICA512 ectodomain. PLoS One. 2011;6(9):e24191. DOI:10.1371/journal.pone.0024191 | PubMed ID:21935384 | HubMed [Primo11]
  3. Noguera ME, Primo ME, Jakoncic J, Poskus E, Solimena M, and Ermácora MR. X-ray structure of the mature ectodomain of phogrin. J Struct Funct Genomics. 2015 Mar;16(1):1-9. DOI:10.1007/s10969-014-9191-0 | PubMed ID:25421040 | HubMed [Noguera15]
  4. Ort T, Voronov S, Guo J, Zawalich K, Froehner SC, Zawalich W, and Solimena M. Dephosphorylation of beta2-syntrophin and Ca2+/mu-calpain-mediated cleavage of ICA512 upon stimulation of insulin secretion. EMBO J. 2001 Aug 1;20(15):4013-23. DOI:10.1093/emboj/20.15.4013 | PubMed ID:11483505 | HubMed [Ort01]
  5. Cai T, Hirai H, Zhang G, Zhang M, Takahashi N, Kasai H, Satin LS, Leapman RD, and Notkins AL. Deletion of Ia-2 and/or Ia-2β in mice decreases insulin secretion by reducing the number of dense core vesicles. Diabetologia. 2011 Sep;54(9):2347-57. DOI:10.1007/s00125-011-2221-6 | PubMed ID:21732083 | HubMed [Cai11]
  6. Fitzgerald LR, Walton KM, Dixon JE, and Largent BL. PTP NE-6: a brain-enriched receptor-type protein tyrosine phosphatase with a divergent catalytic domain. J Neurochem. 1997 May;68(5):1820-9. PubMed ID:9109506 | HubMed [Fitzgerald]
  7. Drake PG, Peters GH, Andersen HS, Hendriks W, and Møller NP. A novel strategy for the development of selective active-site inhibitors of the protein tyrosine phosphatase-like proteins islet-cell antigen 512 (IA-2) and phogrin (IA-2beta). Biochem J. 2003 Jul 15;373(Pt 2):393-401. DOI:10.1042/BJ20021851 | PubMed ID:12697028 | HubMed [Drake]
  8. Caromile LA, Oganesian A, Coats SA, Seifert RA, and Bowen-Pope DF. The neurosecretory vesicle protein phogrin functions as a phosphatidylinositol phosphatase to regulate insulin secretion. J Biol Chem. 2010 Apr 2;285(14):10487-96. DOI:10.1074/jbc.M109.066563 | PubMed ID:20097759 | HubMed [Caromile10]
  9. Rabin DU, Pleasic SM, Shapiro JA, Yoo-Warren H, Oles J, Hicks JM, Goldstein DE, and Rae PM. Islet cell antigen 512 is a diabetes-specific islet autoantigen related to protein tyrosine phosphatases. J Immunol. 1994 Mar 15;152(6):3183-8. PubMed ID:8144912 | HubMed [Rabin94]
  10. Solimena M, Dirkx R Jr, Hermel JM, Pleasic-Williams S, Shapiro JA, Caron L, and Rabin DU. ICA 512, an autoantigen of type I diabetes, is an intrinsic membrane protein of neurosecretory granules. EMBO J. 1996 May 1;15(9):2102-14. PubMed ID:8641276 | HubMed [Solimena96]
  11. Cui L, Yu WP, DeAizpurua HJ, Schmidli RS, and Pallen CJ. Cloning and characterization of islet cell antigen-related protein-tyrosine phosphatase (PTP), a novel receptor-like PTP and autoantigen in insulin-dependent diabetes. J Biol Chem. 1996 Oct 4;271(40):24817-23. PubMed ID:8798755 | HubMed [Cui96]
  12. Lan MS, Lu J, Goto Y, and Notkins AL. Molecular cloning and identification of a receptor-type protein tyrosine phosphatase, IA-2, from human insulinoma. DNA Cell Biol. 1994 May;13(5):505-14. DOI:10.1089/dna.1994.13.505 | PubMed ID:8024693 | HubMed [Lan94]
  13. Trajkovski M, Mziaut H, Altkrüger A, Ouwendijk J, Knoch KP, Müller S, and Solimena M. Nuclear translocation of an ICA512 cytosolic fragment couples granule exocytosis and insulin expression in {beta}-cells. J Cell Biol. 2004 Dec 20;167(6):1063-74. DOI:10.1083/jcb.200408172 | PubMed ID:15596545 | HubMed [Trajkovski04]
  14. Ort T, Maksimova E, Dirkx R, Kachinsky AM, Berghs S, Froehner SC, and Solimena M. The receptor tyrosine phosphatase-like protein ICA512 binds the PDZ domains of beta2-syntrophin and nNOS in pancreatic beta-cells. Eur J Cell Biol. 2000 Sep;79(9):621-30. PubMed ID:11043403 | HubMed [Ort00]
  15. Diez J, Park Y, Zeller M, Brown D, Garza D, Ricordi C, Hutton J, Eisenbarth GS, and Pugliese A. Differential splicing of the IA-2 mRNA in pancreas and lymphoid organs as a permissive genetic mechanism for autoimmunity against the IA-2 type 1 diabetes autoantigen. Diabetes. 2001 Apr;50(4):895-900. PubMed ID:11289059 | HubMed [Diez01]
  16. Kawasaki E, Hutton JC, and Eisenbarth GS. Molecular cloning and characterization of the human transmembrane protein tyrosine phosphatase homologue, phogrin, an autoantigen of type 1 diabetes. Biochem Biophys Res Commun. 1996 Oct 14;227(2):440-7. DOI:10.1006/bbrc.1996.1526 | PubMed ID:8878534 | HubMed [Kawasaki96]
  17. Smith PD, Barker KT, Wang J, Lu YJ, Shipley J, and Crompton MR. ICAAR, a novel member of a new family of transmembrane, tyrosine phosphatase-like proteins. Biochem Biophys Res Commun. 1996 Dec 13;229(2):402-11. DOI:10.1006/bbrc.1996.1817 | PubMed ID:8954911 | HubMed [Smith96]
  18. Sorokin AV, Nair BC, Wei Y, Aziz KE, Evdokimova V, Hung MC, and Chen J. Aberrant Expression of proPTPRN2 in Cancer Cells Confers Resistance to Apoptosis. Cancer Res. 2015 May 1;75(9):1846-58. DOI:10.1158/0008-5472.CAN-14-2718 | PubMed ID:25877877 | HubMed [Sorokin15]
  19. Kim J, Bang H, Ko S, Jung I, Hong H, and Kim-Ha J. Drosophila ia2 modulates secretion of insulin-like peptide. Comp Biochem Physiol A Mol Integr Physiol. 2008 Oct;151(2):180-4. DOI:10.1016/j.cbpa.2008.06.020 | PubMed ID:18634898 | HubMed [Kim]
  20. Zahn TR, Macmorris MA, Dong W, Day R, and Hutton JC. IDA-1, a Caenorhabditis elegans homolog of the diabetic autoantigens IA-2 and phogrin, is expressed in peptidergic neurons in the worm. J Comp Neurol. 2001 Jan 1;429(1):127-43. PubMed ID:11086294 | HubMed [Zahn01]
  21. Cai T, Fukushige T, Notkins AL, and Krause M. Insulinoma-Associated Protein IA-2, a Vesicle Transmembrane Protein, Genetically Interacts with UNC-31/CAPS and Affects Neurosecretion in Caenorhabditis elegans. J Neurosci. 2004 Mar 24;24(12):3115-24. DOI:10.1523/JNEUROSCI.0101-04.2004 | PubMed ID:15044551 | HubMed [Cai04]
  22. Kharitidi D, Manteghi S, and Pause A. Pseudophosphatases: methods of analysis and physiological functions. Methods. 2014 Jan 15;65(2):207-18. DOI:10.1016/j.ymeth.2013.09.009 | PubMed ID:24064037 | HubMed [Kharitidi13]
  23. Kubosaki A, Gross S, Miura J, Saeki K, Zhu M, Nakamura S, Hendriks W, and Notkins AL. Targeted disruption of the IA-2beta gene causes glucose intolerance and impairs insulin secretion but does not prevent the development of diabetes in NOD mice. Diabetes. 2004 Jul;53(7):1684-91. PubMed ID:15220191 | HubMed [Kubosaki04]
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