The human phosphatase interactome: An intricate family portrait

FEBS Letters

Volumn 586, Issue 17, 2012, Pages 2732-2739

  Sacco, Francesca ^a   Perfetto, Livia ^a   Castagnoli, Luisa ^a   Cesareni, Gianni ^a,b  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b IRCCS FONDAZIONE SANTA LUCIA   (Italy)

Author keywords

Human phosphatome; Phosphatase family classification; Substrate recognition specificity

Indexed keywords

ADAPTOR PROTEIN; PHOSPHATASE; PROTEOME;

CARBOXY TERMINAL SEQUENCE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYME SUBSTRATE; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN DEPHOSPHORYLATION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; REVIEW; SEQUENCE HOMOLOGY;

AMINO ACID MOTIFS; BINDING SITES; CATALYTIC DOMAIN; HUMANS; PEPTIDES; PHOSPHORIC MONOESTER HYDROLASES; PHOSPHORYLATION; PHYLOGENY; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY; TYROSINE;

EUKARYOTA;

EID: 84864583212     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2012.05.008     Document Type: Review

References (49)

1. M. Mann, and O.N. Jensen Proteomic analysis of post-translational modifications Nat. Biotechnol. 21 2003 255 261
2. J.D. Graves, and E.G. Krebs Protein phosphorylation and signal transduction Pharmacol. Ther. 82 1999 111 121
3. G. Manning, D.B. Whyte, R. Martinez, T. Hunter, and S. Sudarsanam The protein kinase complement of the human genome Science 298 2002 1912 1934
4. G. Manning, G.D. Plowman, T. Hunter, and S. Sudarsanam Evolution of protein kinase signaling from yeast to man Trends Biochem. Sci. 27 2002 514 520
5. N.K. Tonks Protein tyrosine phosphatases: from genes, to function, to disease Nat. Rev. Mol. Cell Biol. 7 2006 833 846
6. D. Easty, W. Gallagher, and D.C. Bennett Protein tyrosine phosphatases, new targets for cancer therapy Curr. Cancer Drug Targets 6 2006 519 532
7. C.E. Gee, and I.M. Mansuy Protein phosphatases and their potential implications in neuroprotective processes Cell. Mol. Life Sci. 62 2005 1120 1130
8. J.V. Olsen, B. Blagoev, F. Gnad, B. Macek, C. Kumar, P. Mortensen, and M. Mann Global, in vivo, and site-specific phosphorylation dynamics in signaling networks Cell 127 2006 635 648
9. P.V. Hornbeck, J.M. Kornhauser, S. Tkachev, B. Zhang, E. Skrzypek, B. Murray, V. Latham, and M. Sullivan PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse Nucleic Acids Res. 40 2012 D261 D270
10. S. Caenepeel, G. Charydczak, S. Sudarsanam, T. Hunter, and G. Manning The mouse kinome: discovery and comparative genomics of all mouse protein kinases Proc. Natl. Acad. Sci. USA 101 2004 11707 11712
11. H. Zhu Analysis of yeast protein kinases using protein chips Nat. Genet. 26 2000 283 289
12. A. Alonso Protein tyrosine phosphatases in the human genome Cell 117 2004 699 711
13. T. Tiganis, and A.M. Bennett Protein tyrosine phosphatase function: the substrate perspective Biochem. J. 402 2007 1 15
14. J.N. Andersen, P.G. Jansen, S.M. Echwald, O.H. Mortensen, T. Fukada, R. Del Vecchio, N.K. Tonks, and N.P. Moller A genomic perspective on protein tyrosine phosphatases: gene structure, pseudogenes, and genetic disease linkage FASEB J. 18 2004 8 30
15. N.K. Tonks, and B.G. Neel Combinatorial control of the specificity of protein tyrosine phosphatases Curr. Opin. Cell Biol. 13 2001 182 195
16. J. Roy, and M.S. Cyert Cracking the phosphatase code: docking interactions determine substrate specificity Sci. Signal. 2 2009 re9
17. G.B. Moorhead, V. De Wever, G. Templeton, and D. Kerk Evolution of protein phosphatases in plants and animals Biochem J. 417 2009 401 409
18. S. Hunter InterPro in 2011: new developments in the family and domain prediction database Nucleic Acids Res. 40 2012 D306 D312
19. M.A. Larkin Clustal W and Clustal X version 2.0 Bioinformatics 23 2007 2947 2948
20. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
21. Z.Q. Shi, W. Lu, and G.S. Feng The Shp-2 tyrosine phosphatase has opposite effects in mediating the activation of extracellular signal-regulated and c-Jun NH2-terminal mitogen-activated protein kinases J. Biol. Chem. 273 1998 4904 4908
22. A.M. O'Reilly, and B.G. Neel Structural determinants of SHP-2 function and specificity in Xenopus mesoderm induction Mol. Cell. Biol. 18 1998 161 177
23. T. Tenev Both SH2 domains are involved in interaction of SHP-1 with the epidermal growth factor receptor but cannot confer receptor-directed activity to SHP-1/SHP-2 chimera J. Biol. Chem. 272 1997 5966 5973
24. S. Walchli, X. Espanel, A. Harrenga, M. Rossi, G. Cesareni, and R. Hooft van Huijsduijnen Probing protein-tyrosine phosphatase substrate specificity using a phosphotyrosine-containing phage library J. Biol. Chem. 279 2004 311 318
25. A.J. Barr Large-scale structural analysis of the classical human protein tyrosine phosphatome Cell 136 2009 352 363
26. Z.Y. Zhang, A.M. Thieme-Sefler, D. Maclean, D.J. McNamara, E.M. Dobrusin, T.K. Sawyer, and J.E. Dixon Substrate specificity of the protein tyrosine phosphatases Proc. Natl. Acad. Sci USA 90 1993 4446 4450
27. Z.Y. Zhang, D. Maclean, D.J. McNamara, T.K. Sawyer, and J.E. Dixon Protein tyrosine phosphatase substrate specificity: size and phosphotyrosine positioning requirements in peptide substrates Biochemistry 33 1994 2285 2290
28. C. Blanchetot, M. Chagnon, N. Dube, M. Halle, and M.L. Tremblay Substrate-trapping techniques in the identification of cellular PTP targets Methods 35 2005 44 53
29. F. Sacco Tumor suppressor density-enhanced phosphatase-1 (DEP-1) inhibits the RAS pathway by direct dephosphorylation of ERK1/2 kinases J. Biol. Chem. 284 2009 22048 22058
30. E. Ferrari Identification of new substrates of the protein-tyrosine phosphatase PTP1B by Bayesian integration of proteome evidence J. Biol. Chem. 286 2011 4173 4185
31. M. Holgado-Madruga, and A.J. Wong Role of the Grb2-associated binder 1/SHP-2 interaction in cell growth and transformation Cancer Res. 64 2004 2007 2015
32. A. Carlucci Protein-tyrosine phosphatase PTPD1 regulates focal adhesion kinase autophosphorylation and cell migration J. Biol. Chem. 283 2008 10919 10929
33. T. Tiganis, A.M. Bennett, K.S. Ravichandran, and N.K. Tonks Epidermal growth factor receptor and the adaptor protein p52Shc are specific substrates of T-cell protein tyrosine phosphatase Mol. Cell. Biol. 18 1998 1622 1634
34. A.J. Garton, M.R. Burnham, A.H. Bouton, and N.K. Tonks Association of PTP-PEST with the SH3 domain of p130cas; a novel mechanism of protein tyrosine phosphatase substrate recognition Oncogene 15 1997 877 885
35. A. Angers-Loustau, J.F. Cote, A. Charest, D. Dowbenko, S. Spencer, L.A. Lasky, and M.L. Tremblay Protein tyrosine phosphatase-PEST regulates focal adhesion disassembly, migration, and cytokinesis in fibroblasts J. Cell Biol. 144 1999 1019 1031
36. M. Camps, A. Nichols, C. Gillieron, B. Antonsson, M. Muda, C. Chabert, U. Boschert, and S. Arkinstall Catalytic activation of the phosphatase MKP-3 by ERK2 mitogen-activated protein kinase Science 280 1998 1262 1265
37. R. Pulido, A. Zuniga, and A. Ullrich PTP-SL and STEP protein tyrosine phosphatases regulate the activation of the extracellular signal-regulated kinases ERK1 and ERK2 by association through a kinase interaction motif EMBO J. 17 1998 7337 7350
38. L. Ding Genome remodelling in a basal-like breast cancer metastasis and xenograft Nature 464 2010 999 1005
39. F. Cong, S. Spencer, J.F. Cote, Y. Wu, M.L. Tremblay, L.A. Lasky, and S.P. Goff Cytoskeletal protein PSTPIP1 directs the PEST-type protein tyrosine phosphatase to the c-Abl kinase to mediate Abl dephosphorylation Mol. Cell 6 2000 1413 1423
40. B.A. Perrino, L.Y. Ng, and T.R. Soderling Calcium regulation of calcineurin phosphatase activity by its B subunit and calmodulin. Role of the autoinhibitory domain J. Biol. Chem. 270 1995 340 346
41. J. Roy, H. Li, P.G. Hogan, and M.S. Cyert A conserved docking site modulates substrate affinity for calcineurin, signaling output, and in vivo function Mol. Cell 25 2007 889 901
42. J. Jin Eukaryotic protein domains as functional units of cellular evolution Sci. Signal. 2 2009 ra76
43. M. Persico, A. Ceol, C. Gavrila, R. Hoffmann, A. Florio, and G. Cesareni HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms BMC Bioinformatics 6 Suppl 4 2005 S21
44. S. Kerrien The IntAct molecular interaction database in 2012 Nucleic Acids Res. 40 2012 D841 D846
45. S.G. Julien, N. Dube, S. Hardy, and M.L. Tremblay Inside the human cancer tyrosine phosphatome Nat. Rev. Cancer 11 2011 35 49
46. V. Gabarra-Niecko, M.D. Schaller, and J.M. Dunty FAK regulates biological processes important for the pathogenesis of cancer Cancer Metastasis Rev. 22 2003 359 374
47. K.W. Harder, N.P. Moller, J.W. Peacock, and F.R. Jirik Protein-tyrosine phosphatase alpha regulates Src family kinases and alters cell-substratum adhesion J. Biol. Chem. 273 1998 31890 31900
48. J. den Hertog, S. Tracy, and T. Hunter Phosphorylation of receptor protein-tyrosine phosphatase alpha on Tyr789, a binding site for the SH3-SH2-SH3 adaptor protein GRB-2 in vivo EMBO J. 13 1994 3020 3032
49. W. Huang da, B.T. Sherman, and R.A. Lempicki Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat. Protoc. 4 2009 44 57