Protein tyrosine phosphatase

Protein tyrosine phosphatases (EC 3.1.3.48, systematic name protein-tyrosine-phosphate phosphohydrolase) are a group of enzymes that remove phosphate groups from phosphorylated tyrosine residues on proteins:

Protein-tyrosine-phosphatase
Protein tyrosine phosphatase 1, trimer, Human
Identifiers
EC no.3.1.3.48
CAS no.79747-53-8
Databases
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MetaCycmetabolic pathway
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NCBIproteins
[a protein]-tyrosine phosphate + H2O = [a protein]-tyrosine + phosphate

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

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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

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By mechanism

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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

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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] brain ischemia,[12] alcohol use disorder,[13][14] and stress disorders.[15][16] Together these findings indicate that only at optimal levels of PTPN5 is synaptic function unimpaired.

Class II

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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

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Cdc25 phosphatases (dTyr and/or dThr)

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

Class IV

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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 the other three classes.[20]

By location

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

Common elements

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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
SymbolLMWPc
PfamPF01451
InterProIPR017867
SMARTSM00226
SCOP21phr / SCOPe / SUPFAM
CDDcd00115
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
PDB1bvh​, 1c0e​, 1d1p​, 1d1q​, 1d2a​, 1dg9​, 1jf8​, 1jfv​, 1jl3​, 1ljl
Protein-tyrosine phosphatase
 
Structure of Yersinia protein tyrosine phosphatase.[25]
Identifiers
SymbolY_phosphatase
PfamPF00102
Pfam clanCL0031
InterProIPR000242
SMARTSM00194
PROSITEPS50055
SCOP21ypt / SCOPe / SUPFAM
CDDcd00047
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
PDB1a5y​, 1aax​, 1bzc​, 1bzh​, 1bzj​, 1c83​, 1c84​, 1c85​, 1c86​, 1c87
Dual-specificity phosphatase, catalytic domain
 
Structure of the dual-specificity protein phosphatase VHR.[26]
Identifiers
SymbolDSPc
PfamPF00782
Pfam clanCL0031
InterProIPR000340
PROSITEPDOC00323
SCOP21vhr / SCOPe / SUPFAM
CDDcd14498
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
PDB1d5r​, 1i9s​, 1i9t​, 1j4x​, 1m3g​, 1mkp​, 1ohc​, 1ohd​, 1ohe​, 2c46
Protein-tyrosine phosphatase, SIW14-like
 
Structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana.[27]
Identifiers
SymbolY_phosphatase2
PfamPF03162
Pfam clanCL0031
InterProIPR004861
CDDcd14528
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
PDB1xri​, 2q47
Protein-tyrosine phosphatase-like, PTPLA
Identifiers
SymbolPTPLA
PfamPF04387
InterProIPR007482
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

Expression pattern

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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, and differs between brain regions, with no expression in the cerebellum.[29][30][31]

References

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  1. ^ Dixon JE, Denu JM (2018). "Protein tyrosine phosphatases: mechanisms of catalysis and regulation". Curr Opin Chem Biol. 2 (5): 633–41. doi:10.1016/S1367-5931(98)80095-1. PMID 9818190.
  2. ^ Paul S, Lombroso PJ (2020). "Receptor and nonreceptor protein tyrosine phosphatases in the nervous system". Cell. Mol. Life Sci. 60 (11): 2465–82. doi:10.1007/s00018-003-3123-7. PMC 11138652. PMID 14625689. S2CID 10827975.
  3. ^ a b Zhang Y, Kurup P, Xu J, Carty N, Fernandez SM, Nygaard HB, Pittenger C, Greengard P, Strittmatter SM, Nairn AC, Lombroso PJ (Nov 2018). "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. Bibcode:2010PNAS..10719014Z. doi:10.1073/pnas.1013543107. PMC 2973892. PMID 20956308.
  4. ^ a b Goebel-Goody SM, Wilson-Wallis ED, Royston S, Tagliatela SM, Naegele JR, Lombroso PJ (Jul 2019). "Genetic manipulation of STEP reverses behavioral abnormalities in a fragile X syndrome mouse model". Genes, Brain and Behavior. 11 (5): 586–600. doi:10.1111/j.1601-183X.2012.00781.x. PMC 3922131. PMID 22405502.
  5. ^ Kurup P, Zhang Y, Xu J, Venkitaramani DV, Haroutunian V, Greengard P, Nairn AC, Lombroso PJ (Apr 2022). "Abeta-mediated NMDA receptor endocytosis in Alzheimer's disease involves ubiquitination of the tyrosine phosphatase STEP61". The Journal of Neuroscience. 30 (17): 5948–57. doi:10.1523/JNEUROSCI.0157-10.2010. PMC 2868326. PMID 20427654.
  6. ^ Sun JP, Zhang ZY, Wang WQ (2017). "An overview of the protein tyrosine phosphatase superfamily". Curr Top Med Chem. 3 (7): 739–48. doi:10.2174/1568026033452302. PMID 12678841.
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  12. ^ Deb I, Manhas N, Poddar R, Rajagopal S, Allan AM, Lombroso PJ, Rosenberg GA, Candelario-Jalil E, Paul S (Nov 2020). "Neuroprotective role of a brain-enriched tyrosine phosphatase, STEP, in focal cerebral ischemia". The Journal of Neuroscience. 33 (45): 17814–26. doi:10.1523/JNEUROSCI.2346-12.2013. PMC 3818554. PMID 24198371.
  13. ^ Hicklin TR, Wu PH, Radcliffe RA, Freund RK, Goebel-Goody SM, Correa PR, Proctor WR, Lombroso PJ, Browning MD (Apr 2020). "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. Bibcode:2011PNAS..108.6650H. doi:10.1073/pnas.1017856108. PMC 3081035. PMID 21464302.
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  15. ^ Yang CH, Huang CC, Hsu KS (May 2022). "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. doi:10.1523/JNEUROSCI.5902-11.2012. PMC 6703597. PMID 22649233.
  16. ^ Dabrowska J, Hazra R, Guo JD, Li C, Dewitt S, Xu J, Lombroso PJ, Rainnie DG (Dec 2020). "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. doi:10.1016/j.biopsych.2013.07.032. PMC 3818357. PMID 24012328.
  17. ^ Wo YY, Shabanowitz J, Hunt DF, Davis JP, Mitchell GL, Van Etten RL, McCormack AL (2023). "Sequencing, cloning, and expression of human red cell-type acid phosphatase, a cytoplasmic phosphotyrosyl protein phosphatase". J. Biol. Chem. 267 (15): 10856–10865. doi:10.1016/S0021-9258(19)50097-7. 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. doi:10.1002/pro.5560010603. PMC 2142247. PMID 1304913.
  19. ^ Chen MJ, Dixon JE, Manning G (April 2023). "Genomics and evolution of protein phosphatases". Science Signaling. 10 (474): eaag1796. doi:10.1126/scisignal.aag1796. PMID 28400531. S2CID 41041971.
  20. ^ Plaxton WC, McManus MT (2020). Control of primary metabolism in plants. Wiley-Blackwell. pp. 130–. ISBN 978-1-4051-3096-7. Retrieved 12 December 2020.
  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. doi:10.1110/ps.062128706. PMC 2242534. PMID 16672235.
  22. ^ Perrimon N, Johnson MR, Perkins LA, Melnick MB (2018). "The nonreceptor protein tyrosine phosphatase corkscrew functions in multiple receptor tyrosine kinase pathways in Drosophila". Dev. Biol. 180 (1): 63–81. doi:10.1006/dbio.1996.0285. PMID 8948575.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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  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. Bibcode:1994Natur.370..575S. doi:10.1038/370575a0. PMID 8052313. S2CID 4310667.
  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" (PDF). Nature. 370 (6490): 571–5. Bibcode:1994Natur.370..571S. doi:10.1038/370571a0. hdl:2027.42/62819. PMID 8052312. S2CID 4332099.
  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. Bibcode:1996Sci...272.1328Y. doi:10.1126/science.272.5266.1328. PMID 8650541. S2CID 33816598.
  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. doi:10.1002/prot.22041. PMC 4437517. PMID 18433060.
  28. ^ Mustelin T, Vang T, Bottini N (2018). "Protein tyrosine phosphatases and the immune response". Nat. Rev. Immunol. 5 (1): 43–57. doi:10.1038/nri1530. PMID 15630428. S2CID 20308090.
  29. ^ Lombroso PJ, Murdoch G, Lerner M (Aug 2021). "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. Bibcode:1991PNAS...88.7242L. doi:10.1073/pnas.88.16.7242. PMC 52270. PMID 1714595.
  30. ^ Bult A, Zhao F, Dirkx R, Sharma E, Lukacsi E, Solimena M, Naegele JR, Lombroso PJ (Dec 2021). "STEP61: a member of a family of brain-enriched PTPs is localized to the endoplasmic reticulum". The Journal of Neuroscience. 16 (24): 7821–31. doi:10.1523/JNEUROSCI.16-24-07821.1996. PMC 6579237. PMID 8987810.
  31. ^ Lombroso PJ, Naegele JR, Sharma E, Lerner M (Jul 2021). "A protein tyrosine phosphatase expressed within dopaminoceptive neurons of the basal ganglia and related structures". The Journal of Neuroscience. 13 (7): 3064–74. doi:10.1523/JNEUROSCI.13-07-03064.1993. PMC 6576687. PMID 8331384.

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