Protein tyrosine phosphatase

Protein-tyrosine-phosphatase

Protein tyrosine phosphatase 1, trimer, Human
Identifiers
EC number 3.1.3.48
CAS number 79747-53-8
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum

Protein tyrosine phosphatases are a group of enzymes that remove phosphate groups from phosphorylated tyrosine residues on proteins. Protein tyrosine (pTyr) phosphorylation is a common post-translational modification that can create novel recognition motifs for protein interactions and cellular localization, affect protein stability, and regulate enzyme activity. As a consequence, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; EC 3.1.3.48) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation, transformation, and synaptic plasticity.[1][2][3][4]

Functions

Together with tyrosine kinases, PTPs regulate the phosphorylation state of many important signalling molecules, such as the MAP kinase family. PTPs are increasingly viewed as integral components of signal transduction cascades, despite less study and understanding compared to tyrosine kinases.

PTPs have been implicated in regulation of many cellular processes, including, but not limited to:

Classification

By mechanism

PTP activity can be found in four protein families.[6][7]

Links to all 107 members of the protein tyrosine phosphatase family can be found in the template at the bottom of this article.

Class I

The class I PTPs, are the largest group of PTPs with 99 members, which can be further subdivided into

Dual-specificity phosphatases (dTyr and dSer/dThr) dual-specificity protein-tyrosine phosphatases. Ser/Thr and Tyr dual-specificity phosphatases are a group of enzymes with both Ser/Thr (EC 3.1.3.16) and tyrosine-specific protein phosphatase (EC 3.1.3.48) activity able to remove the serine/threonine or the tyrosine-bound phosphate group from a wide range of phosphoproteins, including a number of enzymes that have been phosphorylated under the action of a kinase. Dual-specificity protein phosphatases (DSPs) regulate mitogenic signal transduction and control the cell cycle.

LEOPARD syndrome, Noonan syndrome, and Metachondromatosis are associated with PTPN11.

Elevated levels of activated PTPN5 negatively affects synaptic stability and plays a role in Alzheimer’s disease,[3] Fragile X Syndrome[4] schizophrenia,[8] and Parkinson’s disease.[9] Decreased levels of PTPN5 has been implicated in Huntington's disease,[10][11] cerebral ischemia[12] alcohol abuse,[13][14] and stress disorders.[15][16] Together these findings indicate that only at optimal levels of PTPN5 is synaptic function unimpaired.

Class II

LMW (low-molecular-weight) phosphatases, or acid phosphatases, act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates.[17][18]

The class II PTPs contain only one member, low-molecular-weight phosphotyrosine phosphatase (LMPTP).

Class III

Cdc25 phosphatases (dTyr and/or dThr)

The Class III PTPs contains three members, CDC25 A, B, and C

Class IV

These are members of the HAD fold and superfamily, and include phosphatases specific to pTyr and pSer/Thr as well as small molecule phosphatases and other enzymes.[19] The subfamily EYA (eyes absent) is believed to be pTyr-specific, and has four members in human, EYA1, EYA2, EYA3, and EYA4. This class has a distinct catalytic mechanism from other other three classes.[20]

By location

Based on their cellular localization, PTPases are also classified as:

Common elements

All PTPases, other than those of the eya family, carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and possess a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif.[23] Functional diversity between PTPases is endowed by regulatory domains and subunits.

Low-molecular-weight phosphotyrosine protein phosphatase

Structure of a low-molecular-weight phosphotyrosine protein phosphatase.[24]
Identifiers
Symbol LMWPc
Pfam PF01451
InterPro IPR017867
SMART SM00226
SCOP 1phr
SUPERFAMILY 1phr
Protein-tyrosine phosphatase

Structure of Yersinia protein tyrosine phosphatase.[25]
Identifiers
Symbol Y_phosphatase
Pfam PF00102
Pfam clan CL0031
InterPro IPR000242
SMART SM00194
PROSITE PS50055
SCOP 1ypt
SUPERFAMILY 1ypt
Dual-specificity phosphatase, catalytic domain

Structure of the dual-specificity protein phosphatase VHR.[26]
Identifiers
Symbol DSPc
Pfam PF00782
Pfam clan CL0031
InterPro IPR000340
PROSITE PDOC00323
SCOP 1vhr
SUPERFAMILY 1vhr
Protein-tyrosine phosphatase, SIW14-like

Structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana.[27]
Identifiers
Symbol Y_phosphatase2
Pfam PF03162
Pfam clan CL0031
InterPro IPR004861
Protein-tyrosine phosphatase-like, PTPLA
Identifiers
Symbol PTPLA
Pfam PF04387
InterPro IPR007482

Expression pattern

Individual PTPs may be expressed by all cell types, or their expression may be strictly tissue-specific. Most cells express 30% to 60% of all the PTPs, however hematopoietic and neuronal cells express a higher number of PTPs in comparison to other cell types. T cells and B cells of hematopoietic origin express around 60 to 70 different PTPs. The expression of several PTPS is restricted to hematopoietic cells, for example, LYP, SHP1, CD45, and HePTP.[28] The expression of PTPN5 is restricted to the brain. Differential expression of PTPN5 is found in many brain regions, with no expression in the cerebellum.[29][30][31]

References

  1. ↑ Dixon JE, Denu JM (1998). "Protein tyrosine phosphatases: mechanisms of catalysis and regulation". Curr Opin Chem Biol. 2 (5): 633–41. PMID 9818190.
  2. ↑ Paul S, Lombroso PJ (2003). "Receptor and nonreceptor protein tyrosine phosphatases in the nervous system". Cell. Mol. Life Sci. 60 (11): 2465–82. PMID 14625689. doi:10.1007/s00018-003-3123-7.
  3. 1 2 Zhang Y, Kurup P, Xu J, Carty N, Fernandez SM, Nygaard HB, Pittenger C, Greengard P, Strittmatter SM, Nairn AC, Lombroso PJ (Nov 2010). "Genetic reduction of striatal-enriched tyrosine phosphatase (STEP) reverses cognitive and cellular deficits in an Alzheimer's disease mouse model". Proceedings of the National Academy of Sciences of the United States of America. 107 (44): 19014–9. PMC 2973892 Freely accessible. PMID 20956308. doi:10.1073/pnas.1013543107.
  4. 1 2 Goebel-Goody SM, Wilson-Wallis ED, Royston S, Tagliatela SM, Naegele JR, Lombroso PJ (Jul 2012). "Genetic manipulation of STEP reverses behavioral abnormalities in a fragile X syndrome mouse model". Genes, Brain, and Behavior. 11 (5): 586–600. PMC 3922131 Freely accessible. PMID 22405502. doi:10.1111/j.1601-183X.2012.00781.x.
  5. ↑ Kurup P, Zhang Y, Xu J, Venkitaramani DV, Haroutunian V, Greengard P, Nairn AC, Lombroso PJ (Apr 2010). "Abeta-mediated NMDA receptor endocytosis in Alzheimer's disease involves ubiquitination of the tyrosine phosphatase STEP61". The Journal of Neuroscience. 30 (17): 5948–57. PMC 2868326 Freely accessible. PMID 20427654. doi:10.1523/JNEUROSCI.0157-10.2010.
  6. ↑ Sun JP, Zhang ZY, Wang WQ (2003). "An overview of the protein tyrosine phosphatase superfamily". Curr Top Med Chem. 3 (7): 739–48. PMID 12678841.
  7. ↑ Alonso A, Sasin J, et al. (2004). "Protein tyrosine phosphatases in the human genome". Cell. 117 (6): 699–711. PMID 15186772. doi:10.1016/j.cell.2004.05.018.
  8. ↑ Carty NC, Xu J, Kurup P, Brouillette J, Goebel-Goody SM, Austin DR, Yuan P, Chen G, Correa PR, Haroutunian V, Pittenger C, Lombroso PJ (2012). "The tyrosine phosphatase STEP: implications in schizophrenia and the molecular mechanism underlying antipsychotic medications". Translational Psychiatry. 2 (7): e137. PMC 3410627 Freely accessible. PMID 22781170. doi:10.1038/tp.2012.63.
  9. ↑ Kurup PK, Xu J, Videira RA, Ononenyi C, Baltazar G, Lombroso PJ, Nairn AC (Jan 2015). "STEP61 is a substrate of the E3 ligase parkin and is upregulated in Parkinson's disease". Proceedings of the National Academy of Sciences of the United States of America. 112 (4): 1202–7. PMC 4313846 Freely accessible. PMID 25583483. doi:10.1073/pnas.1417423112.
  10. ↑ Saavedra A, Giralt A, Rué L, Xifró X, Xu J, Ortega Z, Lucas JJ, Lombroso PJ, Alberch J, Pérez-Navarro E (Jun 2011). "Striatal-enriched protein tyrosine phosphatase expression and activity in Huntington's disease: a STEP in the resistance to excitotoxicity". The Journal of Neuroscience. 31 (22): 8150–62. PMC 3472648 Freely accessible. PMID 21632937. doi:10.1523/JNEUROSCI.3446-10.2011.
  11. ↑ Gladding CM, Sepers MD, Xu J, Zhang LY, Milnerwood AJ, Lombroso PJ, Raymond LA (Sep 2012). "Calpain and STriatal-Enriched protein tyrosine phosphatase (STEP) activation contribute to extrasynaptic NMDA receptor localization in a Huntington's disease mouse model". Human Molecular Genetics. 21 (17): 3739–52. PMC 3412376 Freely accessible. PMID 22523092. doi:10.1093/hmg/dds154.
  12. ↑ Deb I, Manhas N, Poddar R, Rajagopal S, Allan AM, Lombroso PJ, Rosenberg GA, Candelario-Jalil E, Paul S (Nov 2013). "Neuroprotective role of a brain-enriched tyrosine phosphatase, STEP, in focal cerebral ischemia". The Journal of Neuroscience. 33 (45): 17814–26. PMC 3818554 Freely accessible. PMID 24198371. doi:10.1523/JNEUROSCI.2346-12.2013.
  13. ↑ Hicklin TR, Wu PH, Radcliffe RA, Freund RK, Goebel-Goody SM, Correa PR, Proctor WR, Lombroso PJ, Browning MD (Apr 2011). "Alcohol inhibition of the NMDA receptor function, long-term potentiation, and fear learning requires striatal-enriched protein tyrosine phosphatase". Proceedings of the National Academy of Sciences of the United States of America. 108 (16): 6650–5. PMC 3081035 Freely accessible. PMID 21464302. doi:10.1073/pnas.1017856108.
  14. ↑ Darcq E, Hamida SB, Wu S, Phamluong K, Kharazia V, Xu J, Lombroso P, Ron D (Jun 2014). "Inhibition of striatal-enriched tyrosine phosphatase 61 in the dorsomedial striatum is sufficient to increased ethanol consumption". Journal of Neurochemistry. 129 (6): 1024–34. PMC 4055745 Freely accessible. PMID 24588427. doi:10.1111/jnc.12701.
  15. ↑ Yang CH, Huang CC, Hsu KS (May 2012). "A critical role for protein tyrosine phosphatase nonreceptor type 5 in determining individual susceptibility to develop stress-related cognitive and morphological changes". The Journal of Neuroscience. 32 (22): 7550–62. PMID 22649233. doi:10.1523/JNEUROSCI.5902-11.2012.
  16. ↑ Dabrowska J, Hazra R, Guo JD, Li C, Dewitt S, Xu J, Lombroso PJ, Rainnie DG (Dec 2013). "Striatal-enriched protein tyrosine phosphatase-STEPs toward understanding chronic stress-induced activation of corticotrophin releasing factor neurons in the rat bed nucleus of the stria terminalis". Biological Psychiatry. 74 (11): 817–26. PMC 3818357 Freely accessible. PMID 24012328. doi:10.1016/j.biopsych.2013.07.032.
  17. ↑ Wo YY, Shabanowitz J, Hunt DF, Davis JP, Mitchell GL, Van Etten RL, McCormack AL (1992). "Sequencing, cloning, and expression of human red cell-type acid phosphatase, a cytoplasmic phosphotyrosyl protein phosphatase". J. Biol. Chem. 267 (15): 10856–10865. PMID 1587862.
  18. ↑ Shekels LL, Smith AJ, Bernlohr DA, Van Etten RL (1992). "Identification of the adipocyte acid phosphatase as a PAO-sensitive tyrosyl phosphatase". Protein Sci. 1 (6): 710–721. PMC 2142247 Freely accessible. PMID 1304913. doi:10.1002/pro.5560010603.
  19. ↑ Mark J. Chen, Jack E. Dixon & Gerard Manning (2017). "Genomics and evolution of protein phosphatases". Science signaling. 10 (474). PMID 28400531. doi:10.1126/scisignal.aag1796.
  20. ↑ William C. Plaxton; Michael T. McManus (2006). Control of primary metabolism in plants. Wiley-Blackwell. pp. 130–. ISBN 978-1-4051-3096-7. Retrieved 12 December 2010.
  21. ↑ Knapp S, Longman E, Debreczeni JE, Eswaran J, Barr AJ (2006). "The crystal structure of human receptor protein tyrosine phosphatase kappa phosphatase domain 1". Protein Sci. 15 (6): 1500–1505. PMC 2242534 Freely accessible. PMID 16672235. doi:10.1110/ps.062128706.
  22. ↑ Perrimon N, Johnson MR, Perkins LA, Melnick MB (1996). "The nonreceptor protein tyrosine phosphatase corkscrew functions in multiple receptor tyrosine kinase pathways in Drosophila". Dev. Biol. 180 (1): 63–81. PMID 8948575. doi:10.1006/dbio.1996.0285.
  23. ↑ Barford D, Das AK, Egloff MP (1998). "The structure and mechanism of protein phosphatase s: insights into catalysis and regulation". Annu. Rev. Biophys. Biomol. Struct. 27 (1): 133–64. PMID 9646865. doi:10.1146/annurev.biophys.27.1.133.
  24. ↑ Su XD, Taddei N, Stefani M, Ramponi G, Nordlund P (August 1994). "The crystal structure of a low-molecular-weight phosphotyrosine protein phosphatase". Nature. 370 (6490): 575–8. PMID 8052313. doi:10.1038/370575a0.
  25. ↑ Stuckey JA, Schubert HL, Fauman EB, Zhang ZY, Dixon JE, Saper MA (August 1994). "Crystal structure of Yersinia protein tyrosine phosphatase at 2.5 A and the complex with tungstate". Nature. 370 (6490): 571–5. PMID 8052312. doi:10.1038/370571a0.
  26. ↑ Yuvaniyama J, Denu JM, Dixon JE, Saper MA (May 1996). "Crystal structure of the dual specificity protein phosphatase VHR". Science. 272 (5266): 1328–31. PMID 8650541. doi:10.1126/science.272.5266.1328.
  27. ↑ Aceti DJ, Bitto E, Yakunin AF, et al. (October 2008). "Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000". Proteins. 73 (1): 241–53. PMID 18433060. doi:10.1002/prot.22041.
  28. ↑ Mustelin T, Vang T, Bottini N (2005). "Protein tyrosine phosphatases and the immune response". Nat. Rev. Immunol. 5 (1): 43–57. PMID 15630428. doi:10.1038/nri1530.
  29. ↑ Lombroso PJ, Murdoch G, Lerner M (Aug 1991). "Molecular characterization of a protein-tyrosine-phosphatase enriched in striatum". Proceedings of the National Academy of Sciences of the United States of America. 88 (16): 7242–6. PMC 52270 Freely accessible. PMID 1714595. doi:10.1073/pnas.88.16.7242.
  30. ↑ Bult A, Zhao F, Dirkx R, Sharma E, Lukacsi E, Solimena M, Naegele JR, Lombroso PJ (Dec 1996). "STEP61: a member of a family of brain-enriched PTPs is localized to the endoplasmic reticulum". The Journal of Neuroscience. 16 (24): 7821–31. PMID 8987810.
  31. ↑ Lombroso PJ, Naegele JR, Sharma E, Lerner M (Jul 1993). "A protein tyrosine phosphatase expressed within dopaminoceptive neurons of the basal ganglia and related structures". The Journal of Neuroscience. 13 (7): 3064–74. PMID 8331384.

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