Phosphatase Subfamily PTPN12

Phosphatase Classification: Fold CC1:Superfamily CC1: Family PTP: Subfamily PTPN12 (PTP-PEST)

Domain

Phosphatase domain has crystal structure solved [1].

The noncatalytic domain of PTPN22/LYP contains four proline-rich potential SH3 domain binding sites and an NXXY motif that, if phosphorylated, may be recognized by phosphotyrosine binding (PTB) domains [2].

The region of 301-320 in PTPN22 interactions with its phosphatase domain and reduces its catalytic activity [3].

Functions

PTPN12 (PTP-PEST/PTPG1)

PTPN12 is widely expressed in different tissues and at relatively low level in brain (GTEx).

PTPN18 (BDP1/PTP-HSCF)

PTPN18 is most abundantly expressed in spleen (GTEx).

PTPN22 (LYP/PEP/PTPN8)

PTPN22 predominantly in hematopoietic tissues

PTPN22 mainly functions in immune system, particularly its R620W variant associated with many autoimmune diseases. PTPN22 is expressed in certain tissues and cell types, including EBV-transformed lymphocytes, whole blood, spleen and small intestine - terminal ileum (GTEx). Northern blot analysis found PTPN22 to be expressed predominantly in hematopoietic tissue, including spleen, lymph node, thymus, peripheral blood leukocytes, bone marrow, and fetal liver [4], in consistent with earlier study [2].

PTPN22 is expressed in macrophages and plays a critical role in regulating macrophage activation and polarization [5].

R620W variant associated with multiple autoimmune diseases

Missense single-nucleotide polymorphism (SNP) R620W is associated with different autoimmune diseases [6, 7, 8, 9], including rheumatoid arthritis (RA) [10, 11, 12, 13], systemic lupus erythematosus (SLE) [12, 14, 15], type 1 diabetes (T1D) [6], Hashimoto thyroiditis [6], juvenile idiopathic arthritis (JIA) [16], Grave's disease (GD) [16]. However, multiple sclerosis (MS) did not show association with R620W [6].

PTPN22 R620W variant is associated with reduced activation, proliferation and IL-2 production in CD4(+)T cells among T1D patients, and PTPN22 R620W has higher catalytic activity and is a more potent negative regulator of T lymphocyte activation [17, 18]. Thus, R620W is a gain-of-function mutant.

One model behind is as following. R620 locates in a proline-rich sequence in PTPN22, which mediates the interaction between PTPN22 and tyrosine kinase CSK. The R620W variation disrupts not only the interaction between PTPN22 and CSK, but also that between PTPN22 and PTPN22's substrate Src kinase Lck, since PTPN22 constitutively interacts with Lck in a CSK-dependent manner. Lck is not only the substrate of PTPN22, but also phosphorylates PTPN22 at Tyr-536, playing an inhibitory role on the phosphatase activity [19]. Thus, the R620W variation disrupts the interaction between PTPN22 and Lck, leading to reduced phosphorylation at Tyr-536 of PTPN22, which ultimately contributes to gain-of-function inhibition of T cell signaling [19].

Substrates

• Lck (lymphocyte-specific protein tyrosine kinase), a protein found inside specialized cells of the immune system called lymphocytes. Native PTPN22 dephosphorylated Lck at its activating tyrosine residue Tyr-394, but not at the regulatory tyrosine Tyr-505 [20]. On the other hand, Lck phosphorylates PTPN22 at Tyr-536, playing an inhibitory role on the phosphatase activity [19]. Lck is a member of TK group, Src family and SrcB subfamily according to KinBase. Other members in SrcB include LYN, BLK and HCK (note: can they be PTPN22's substrates?).

• ZAP70 (Zeta-chain-associated protein kinase 70), a protein normally expressed near the surface membrane of T cells and natural killer cells. It is part of the T cell receptor, and plays a critical role in T-cell signaling. Native PTPN22 dephosphorylated ZAP70 at its activating tyrosine residue Tyr-493, but not at the regulatory tyrosine Tyr-319 [20]. ZAP70 is a member of TK group, Syk family in KinBase. Another member in Syk family is SYK (note: can it be PTPN22's substrates?).

• VAV, a proto-oncogene that is a member of the Dbl family of guanine nucleotide exchange factors (GEF) for the Rho family of GTP binding proteins. The protein is important in hematopoiesis, playing a role in T-cell and B-cell development and activation [20].

• CD3epsilon, together with CD3-gamma, -delta and -zeta, and the T-cell receptor alpha/beta and gamma/delta heterodimers, forms the T cell receptor-CD3 complex. This complex plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways [20].

• T cell antigen receptor (TCR) zeta, a subunit of T cell receptor-CD3 complex. It plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways [20].

• (Src kinase-associated phosphoprotein 2) [21]

• Valosin containing protein. a type II member of AAA+-ATPase family. It functions as a ubiquitin segregase that remodels multimeric protein complexes by extracting polyubiquitinated proteins for recycling or degradation by the proteasome [20].

Interacting partners

PTPN22 interacts with tyrosine kinase CSK via PTPN22's proline-rich sequence and CSK's SH3 domain [22, 23].

PTPN22 interacts with adaptor molecule Grb2 at Grb2's N-terminal SH3 domain [4]. (SH3 bind to proline-rich sequence of PTPN22?)

PTPN22 is phosphorylated exclusively at Ser-35 by PKC both in vitro and in vivo. The status of Ser-35 phosphorylation may dictate the conformational state of the insert region and thus PTPN22 substrate recognition. Ser-35 phosphorylation impairs PTPN22 to inactivate the Src family kinases and down-regulate T cell receptor signaling [24].

References

1. Tsai SJ, Sen U, Zhao L, Greenleaf WB, Dasgupta J, Fiorillo E, Orrú V, Bottini N, and Chen XS. Crystal structure of the human lymphoid tyrosine phosphatase catalytic domain: insights into redox regulation . Biochemistry. 2009 Jun 9;48(22):4838-45. DOI:10.1021/bi900166y |
2. Cohen S, Dadi H, Shaoul E, Sharfe N, and Roifman CM. Cloning and characterization of a lymphoid-specific, inducible human protein tyrosine phosphatase, Lyp. Blood. 1999 Mar 15;93(6):2013-24.
3. Liu Y, Stanford SM, Jog SP, Fiorillo E, Orrú V, Comai L, and Bottini N. Regulation of lymphoid tyrosine phosphatase activity: inhibition of the catalytic domain by the proximal interdomain. Biochemistry. 2009 Aug 11;48(31):7525-32. DOI:10.1021/bi900332f |
4. Hill RJ, Zozulya S, Lu YL, Ward K, Gishizky M, and Jallal B. The lymphoid protein tyrosine phosphatase Lyp interacts with the adaptor molecule Grb2 and functions as a negative regulator of T-cell activation. Exp Hematol. 2002 Mar;30(3):237-44. DOI:10.1016/s0301-472x(01)00794-9 |
5. Chang HH, Miaw SC, Tseng W, Sun YW, Liu CC, Tsao HW, and Ho IC. PTPN22 modulates macrophage polarization and susceptibility to dextran sulfate sodium-induced colitis. J Immunol. 2013 Sep 1;191(5):2134-43. DOI:10.4049/jimmunol.1203363 |
6. Criswell LA, Pfeiffer KA, Lum RF, Gonzales B, Novitzke J, Kern M, Moser KL, Begovich AB, Carlton VE, Li W, Lee AT, Ortmann W, Behrens TW, and Gregersen PK. Analysis of families in the multiple autoimmune disease genetics consortium (MADGC) collection: the PTPN22 620W allele associates with multiple autoimmune phenotypes. Am J Hum Genet. 2005 Apr;76(4):561-71. DOI:10.1086/429096 |
7. Bottini N, Vang T, Cucca F, and Mustelin T. Role of PTPN22 in type 1 diabetes and other autoimmune diseases. Semin Immunol. 2006 Aug;18(4):207-13. DOI:10.1016/j.smim.2006.03.008 |
8. Vang T, Miletic AV, Bottini N, and Mustelin T. Protein tyrosine phosphatase PTPN22 in human autoimmunity. Autoimmunity. 2007 Sep;40(6):453-61. DOI:10.1080/08916930701464897 |
9. Stanford SM and Bottini N. PTPN22: the archetypal non-HLA autoimmunity gene. Nat Rev Rheumatol. 2014 Oct;10(10):602-11. DOI:10.1038/nrrheum.2014.109 |
10. Begovich AB, Carlton VE, Honigberg LA, Schrodi SJ, Chokkalingam AP, Alexander HC, Ardlie KG, Huang Q, Smith AM, Spoerke JM, Conn MT, Chang M, Chang SY, Saiki RK, Catanese JJ, Leong DU, Garcia VE, McAllister LB, Jeffery DA, Lee AT, Batliwalla F, Remmers E, Criswell LA, Seldin MF, Kastner DL, Amos CI, Sninsky JJ, and Gregersen PK. A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am J Hum Genet. 2004 Aug;75(2):330-7. DOI:10.1086/422827 |
11. Plenge RM, Padyukov L, Remmers EF, Purcell S, Lee AT, Karlson EW, Wolfe F, Kastner DL, Alfredsson L, Altshuler D, Gregersen PK, Klareskog L, and Rioux JD. Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. Am J Hum Genet. 2005 Dec;77(6):1044-60. DOI:10.1086/498651 |
12. Orozco G, Sánchez E, González-Gay MA, López-Nevot MA, Torres B, Cáliz R, Ortego-Centeno N, Jiménez-Alonso J, Pascual-Salcedo D, Balsa A, de Pablo R, Nuñez-Roldan A, González-Escribano MF, and Martín J. Association of a functional single-nucleotide polymorphism of PTPN22, encoding lymphoid protein phosphatase, with rheumatoid arthritis and systemic lupus erythematosus. Arthritis Rheum. 2005 Jan;52(1):219-24. DOI:10.1002/art.20771 |
13. Michou L, Lasbleiz S, Rat AC, Migliorini P, Balsa A, Westhovens R, Barrera P, Alves H, Pierlot C, Glikmans E, Garnier S, Dausset J, Vaz C, Fernandes M, Petit-Teixeira E, Lemaire I, Pascual-Salcedo D, Bombardieri S, Dequeker J, Radstake TR, Van Riel P, van de Putte L, Lopes-Vaz A, Prum B, Bardin T, Dieudé P, Cornélis F, and European Consortium on Rheumatoid Arthritis Families. Linkage proof for PTPN22, a rheumatoid arthritis susceptibility gene and a human autoimmunity gene. Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1649-54. DOI:10.1073/pnas.0610250104 |
14. Kyogoku C, Langefeld CD, Ortmann WA, Lee A, Selby S, Carlton VE, Chang M, Ramos P, Baechler EC, Batliwalla FM, Novitzke J, Williams AH, Gillett C, Rodine P, Graham RR, Ardlie KG, Gaffney PM, Moser KL, Petri M, Begovich AB, Gregersen PK, and Behrens TW. Genetic association of the R620W polymorphism of protein tyrosine phosphatase PTPN22 with human SLE. Am J Hum Genet. 2004 Sep;75(3):504-7. DOI:10.1086/423790 |
15. Smyth D, Cooper JD, Collins JE, Heward JM, Franklyn JA, Howson JM, Vella A, Nutland S, Rance HE, Maier L, Barratt BJ, Guja C, Ionescu-Tîrgoviste C, Savage DA, Dunger DB, Widmer B, Strachan DP, Ring SM, Walker N, Clayton DG, Twells RC, Gough SC, and Todd JA. Replication of an association between the lymphoid tyrosine phosphatase locus (LYP/PTPN22) with type 1 diabetes, and evidence for its role as a general autoimmunity locus. Diabetes. 2004 Nov;53(11):3020-3. DOI:10.2337/diabetes.53.11.3020 |
16. Lee YH, Rho YH, Choi SJ, Ji JD, Song GG, Nath SK, and Harley JB. The PTPN22 C1858T functional polymorphism and autoimmune diseases--a meta-analysis. Rheumatology (Oxford). 2007 Jan;46(1):49-56. DOI:10.1093/rheumatology/kel170 |
17. Vang T, Congia M, Macis MD, Musumeci L, Orrú V, Zavattari P, Nika K, Tautz L, Taskén K, Cucca F, Mustelin T, and Bottini N. Autoimmune-associated lymphoid tyrosine phosphatase is a gain-of-function variant. Nat Genet. 2005 Dec;37(12):1317-9. DOI:10.1038/ng1673 |
18. Aarnisalo J, Treszl A, Svec P, Marttila J, Oling V, Simell O, Knip M, Körner A, Madacsy L, Vasarhelyi B, Ilonen J, and Hermann R. Reduced CD4+T cell activation in children with type 1 diabetes carrying the PTPN22/Lyp 620Trp variant. J Autoimmun. 2008 Aug;31(1):13-21. DOI:10.1016/j.jaut.2008.01.001 |
20. Wu J, Katrekar A, Honigberg LA, Smith AM, Conn MT, Tang J, Jeffery D, Mortara K, Sampang J, Williams SR, Buggy J, and Clark JM. Identification of substrates of human protein-tyrosine phosphatase PTPN22. J Biol Chem. 2006 Apr 21;281(16):11002-10. DOI:10.1074/jbc.M600498200 |
21. Yu X, Chen M, Zhang S, Yu ZH, Sun JP, Wang L, Liu S, Imasaki T, Takagi Y, and Zhang ZY. Substrate specificity of lymphoid-specific tyrosine phosphatase (Lyp) and identification of Src kinase-associated protein of 55 kDa homolog (SKAP-HOM) as a Lyp substrate. J Biol Chem. 2011 Sep 2;286(35):30526-30534. DOI:10.1074/jbc.M111.254722 |
22. Gregorieff A, Cloutier JF, and Veillette A. Sequence requirements for association of protein-tyrosine phosphatase PEP with the Src homology 3 domain of inhibitory tyrosine protein kinase p50(csk). J Biol Chem. 1998 May 22;273(21):13217-22. DOI:10.1074/jbc.273.21.13217 |
23. de la Puerta ML, Trinidad AG, Rodríguez Mdel C, de Pereda JM, Sánchez Crespo M, Bayón Y, and Alonso A. The autoimmunity risk variant LYP-W620 cooperates with CSK in the regulation of TCR signaling. PLoS One. 2013;8(1):e54569. DOI:10.1371/journal.pone.0054569 |
24. Yu X, Sun JP, He Y, Guo X, Liu S, Zhou B, Hudmon A, and Zhang ZY. Structure, inhibitor, and regulatory mechanism of Lyp, a lymphoid-specific tyrosine phosphatase implicated in autoimmune diseases. Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19767-72. DOI:10.1073/pnas.0706233104 |

Supplementary information

Below are the sequences used for position.

>PTPN22 MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFIKGVYGPKAYIATQGPLSTTLLDFWRMIWEYSVLIIVMACMEYEMGKKKCERYWAEPGEMQLEFGPFSVSCEAEKRKSDYIIRTLKVKFNSETRTIYQFHYKNWPDHDVPSSIDPILELIWDVRCYQEDDSVPICIHCSAGCGRTGVICAIDYTWMLLKDGIIPENFSVFSLIREMRTQRPSLVQTQEQYELVYNAVLELFKRQMDVIRDKHSGTESQAKHCIPEKNHTLQADSYSPNLPKSTTKAAKMMNQQRTKMEIKESSSFDFRTSEISAKEELVLHPAKSSTSFDFLELNYSFDKNADTTMKWQTKAFPIVGEPLQKHQSLDLGSLLFEGCSNSKPVNAAGRYFNSKVPITRTKSTPFELIQQRETKEVDSKENFSYLESQPHDSCFVEMQAQKVMHVSSAELNYSLPYDSKHQIRNASNVKHHDSSALGVYSYIPLVENPYFSSWPPSGTSSKMSLDLPEKQDGTVFPSSLLPTSSTSLFSYYNSHDSLSLNSPTNISSLLNQESAVLATAPRIDDEIPPPLPVRTPESFIVVEEAGEFSPNVPKSLSSAVKVKIGTSLEWGGTSEPKKFDDSVILRPSKSVKLRSPKSELHQDRSSPPPPLPERTLESFFLADEDCMQAQSIETYSTSYPDTMENSTSSKQTLKTPGKSFTRSKSLKILRNMKKSICNSCPPNKPAESVQSNNSSSFLNFGFANRFSKPKGPRNPPPTWNI