351
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Vacaru AM, den Hertog J. Catalytically active membrane-distal phosphatase domain of receptor protein-tyrosine phosphatase alpha is required for Src activation. FEBS J 2010; 277:1562-70. [PMID: 20158519 DOI: 10.1111/j.1742-4658.2010.07584.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Receptor protein-tyrosine phosphatase alpha (RPTPalpha) is a transmembrane protein with tandem cytoplasmic phosphatase domains. Most of the catalytic activity is contained by the membrane-proximal catalytic domain (D1). We found a spontaneous Arg554 to His mutation in the pTyr recognition loop of the membrane-distal phosphatase domain (D2) of a human patient. This mutation was not linked to the disease. Here, we report that the R554H mutation abolished RPTPalpha-D2 catalytic activity. The R554H mutation impaired Src binding to RPTPalpha. RPTPalpha, with a catalytic site cysteine to serine mutation in D2, also displayed diminished binding to Src. Concomitant with decreased Src binding of the R554H and C723S mutants compared with wild-type RPTPalpha, enhanced phosphorylation of the inhibitory Src Tyr527 site was observed, as well as reduced Src activation. To confirm that catalytic activity of RPTPalpha-D2 was required for these effects, we analyzed a third mutant, RPTPalpha-R729K, which had an inactive D2. Again, Src binding was reduced and Tyr527 phosphorylation was enhanced. Our results suggest that a catalytically active D2 is required for RPTPalpha to bind and dephosphorylate its well-characterized substrate, Src.
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Affiliation(s)
- Andrei M Vacaru
- Hubrecht Institute - KNAW and University Medical Center, Utrecht, the Netherlands
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352
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The protein tyrosine phosphatases PTPRZ and PTPRG bind to distinct members of the contactin family of neural recognition molecules. Proc Natl Acad Sci U S A 2010; 107:2443-8. [PMID: 20133774 DOI: 10.1073/pnas.0911235107] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The receptor protein tyrosine phosphatases gamma (PTPRG) and zeta (PTPRZ) are expressed primarily in the nervous system and mediate cell adhesion and signaling events during development. We report here the crystal structures of the carbonic anhydrase-like domains of PTPRZ and PTPRG and show that these domains interact directly with the second and third immunoglobulin repeats of the members of the contactin (CNTN) family of neural recognition molecules. Interestingly, these receptors exhibit distinct specificities: PTPRZ binds only to CNTN1, whereas PTPRG interacts with CNTN3, 4, 5, and 6. Furthermore, we present crystal structures of the four N-terminal immunoglobulin repeats of mouse CNTN4 both alone and in complex with the carbonic anhydrase-like domain of mouse PTPRG. In these structures, the N-terminal region of CNTN4 adopts a horseshoe-like conformation found also in CNTN2 and most likely in all CNTNs. This restrained conformation of the second and third immunoglobulin domains creates a binding site that is conserved among CNTN3, 4, 5, and 6. This site contacts a discrete region of PTPRG composed primarily of an extended beta-hairpin loop found in both PTPRG and PTPRZ. Overall, these findings implicate PTPRG, PTPRZ and CNTNs as a group of receptors and ligands involved in the manifold recognition events that underlie the construction of neural networks.
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353
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Tong Y, Hota PK, Penachioni JY, Hamaneh MB, Kim S, Alviani RS, Shen L, He H, Tempel W, Tamagnone L, Park HW, Buck M. Structure and function of the intracellular region of the plexin-b1 transmembrane receptor. J Biol Chem 2010; 284:35962-72. [PMID: 19843518 DOI: 10.1074/jbc.m109.056275] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Members of the plexin family are unique transmembrane receptors in that they interact directly with Rho family small GTPases; moreover, they contain a GTPase-activating protein (GAP) domain for R-Ras, which is crucial for plexin-mediated regulation of cell motility. However, the functional role and structural basis of the interactions between the different intracellular domains of plexins remained unclear. Here we present the 2.4 A crystal structure of the complete intracellular region of human plexin-B1. The structure is monomeric and reveals that the GAP domain is folded into one structure from two segments, separated by the Rho GTPase binding domain (RBD). The RBD is not dimerized, as observed previously. Instead, binding of a conserved loop region appears to compete with dimerization and anchors the RBD to the GAP domain. Cell-based assays on mutant proteins confirm the functional importance of this coupling loop. Molecular modeling based on structural homology to p120(GAP).H-Ras suggests that Ras GTPases can bind to the plexin GAP region. Experimentally, we show that the monomeric intracellular plexin-B1 binds R-Ras but not H-Ras. These findings suggest that the monomeric form of the intracellular region is primed for GAP activity and extend a model for plexin activation.
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Affiliation(s)
- Yufeng Tong
- Departments of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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354
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Greig IR. The analysis of enzymic free energy relationships using kinetic and computational models. Chem Soc Rev 2010; 39:2272-301. [DOI: 10.1039/b902741f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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355
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Vidović D, Schürer SC. Knowledge-based characterization of similarity relationships in the human protein-tyrosine phosphatase family for rational inhibitor design. J Med Chem 2009; 52:6649-59. [PMID: 19810703 DOI: 10.1021/jm9008899] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine phosphorylation, controlled by the coordinated action of protein-tyrosine kinases (PTKs) and protein-tyrosine phosphatases (PTPs), is a fundamental regulatory mechanism of numerous physiological processes. PTPs are implicated in a number of human diseases, and their potential as prospective drug targets is increasingly being recognized. Despite their biological importance, until now no comprehensive overview has been reported describing how all members of the human PTP family are related. Here we review the entire human PTP family and present a systematic knowledge-based characterization of global and local similarity relationships, which are relevant for the development of small molecule inhibitors. We use parallel homology modeling to expand the current PTP structure space and analyze the human PTPs based on local three-dimensional catalytic sites and domain sequences. Furthermore, we demonstrate the importance of binding site similarities in understanding cross-reactivity and inhibitor selectivity in the design of small molecule inhibitors.
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Affiliation(s)
- Dusica Vidović
- Center for Computational Science, University of Miami, Miami, Florida 33136, USA
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356
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Combs AP. Recent Advances in the Discovery of Competitive Protein Tyrosine Phosphatase 1B Inhibitors for the Treatment of Diabetes, Obesity, and Cancer. J Med Chem 2009; 53:2333-44. [DOI: 10.1021/jm901090b] [Citation(s) in RCA: 253] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andrew P. Combs
- Incyte Corporation, Experimental Station, E336/131A, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
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357
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Wu S, Vossius S, Rahmouni S, Miletic AV, Vang T, Vazquez-Rodriguez J, Cerignoli F, Arimura Y, Williams S, Hayes T, Moutschen M, Vasile S, Pellecchia M, Mustelin T, Tautz L. Multidentate small-molecule inhibitors of vaccinia H1-related (VHR) phosphatase decrease proliferation of cervix cancer cells. J Med Chem 2009; 52:6716-23. [PMID: 19888758 PMCID: PMC2790023 DOI: 10.1021/jm901016k] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Loss of VHR phosphatase causes cell cycle arrest in HeLa carcinoma cells, suggesting that VHR inhibition may be a useful approach to halt the growth of cancer cells. We recently reported that VHR is upregulated in several cervix cancer cell lines as well as in carcinomas of the uterine cervix. Here we report the development of multidentate small-molecule inhibitors of VHR that inhibit its enzymatic activity at nanomolar concentrations and exhibit antiproliferative effects on cervix cancer cells. Chemical library screening was used to identify hit compounds, which were further prioritized in profiling and kinetic experiments. SAR analysis was applied in the search for analogs with improved potency and selectivity, resulting in the discovery of novel inhibitors that are able to interact with both the phosphate-binding pocket and several distinct hydrophobic regions within VHR's active site. This multidentate binding mode was confirmed by X-ray crystallography. The inhibitors decreased the proliferation of cervix cancer cells, while growth of primary normal keratinocytes was not affected. These compounds may be a starting point to develop drugs for the treatment of cervical cancer.
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Affiliation(s)
- Shuangding Wu
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Sofie Vossius
- Immunology and Infectious Diseases Unit, GIGA-R, Liège University, Liège, Belgium
| | - Souad Rahmouni
- Immunology and Infectious Diseases Unit, GIGA-R, Liège University, Liège, Belgium
| | - Ana V. Miletic
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Torkel Vang
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Jesus Vazquez-Rodriguez
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Fabio Cerignoli
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Yutaka Arimura
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Scott Williams
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Tikva Hayes
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Michel Moutschen
- Immunology and Infectious Diseases Unit, GIGA-R, Liège University, Liège, Belgium
| | - Stefan Vasile
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Maurizio Pellecchia
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Tomas Mustelin
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Lutz Tautz
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
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358
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Weigelt J. The case for open-access chemical biology. A strategy for pre-competitive medicinal chemistry to promote drug discovery. EMBO Rep 2009; 10:941-5. [PMID: 19721463 DOI: 10.1038/embor.2009.193] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Johan Weigelt
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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359
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The receptor protein tyrosine phosphatase LAR promotes R7 photoreceptor axon targeting by a phosphatase-independent signaling mechanism. Proc Natl Acad Sci U S A 2009; 106:19399-404. [PMID: 19889974 DOI: 10.1073/pnas.0903961106] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Receptor protein tyrosine phosphatases (RPTPs) control many aspects of nervous system development. At the Drosophila neuromuscular junction (NMJ), regulation of synapse growth and maturation by the RPTP LAR depends on catalytic phosphatase activity and on the extracellular ligands Syndecan and Dally-like. We show here that the function of LAR in controlling R7 photoreceptor axon targeting in the visual system differs in several respects. The extracellular domain of LAR important for this process is distinct from the domains known to bind Syndecan and Dally-like, suggesting the involvement of a different ligand. R7 targeting does not require LAR phosphatase activity, but instead depends on the phosphatase activity of another RPTP, PTP69D. In addition, a mutation that prevents dimerization of the intracellular domain of LAR interferes with its ability to promote R7 targeting, although it does not disrupt phosphatase activity or neuromuscular synapse growth. We propose that LAR function in R7 is independent of its phosphatase activity, but requires structural features that allow dimerization and may promote the assembly of downstream effectors.
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360
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Soulsby M, Bennett AM. Physiological Signaling Specificity by Protein Tyrosine Phosphatases. Physiology (Bethesda) 2009; 24:281-9. [DOI: 10.1152/physiol.00017.2009] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Protein tyrosine phosphatases (PTPs) are now recognized to be involved in a multitude of signaling events that control fundamental biological processes such as cell growth, differentiation, apoptosis, and cell movement. PTPs, which were initially thought to be less discriminating in their actions compared with their protein tyrosine kinase counterparts, are now known to regulate these various biological processes in a precise manner. This review will focus on the concept that PTPs exhibit remarkable signaling specificity through intrinsic differences between their PTP domains and through various modes of regulation that endows them with the capacity to promote unique physiological responses.
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Affiliation(s)
- Matthew Soulsby
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut
| | - Anton M. Bennett
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut
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361
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Hower AE, Beltran PJ, Bixby JL. Dimerization of tyrosine phosphatase PTPRO decreases its activity and ability to inactivate TrkC. J Neurochem 2009; 110:1635-47. [PMID: 19573017 DOI: 10.1111/j.1471-4159.2009.06261.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Receptor-protein tyrosine phosphatases (RPTPs), like receptor tyrosine kinases, regulate neuronal differentiation. While receptor tyrosine kinases are dimerized and activated by extracellular ligands, the extent to which RPTPs dimerize, and the effects of dimerization on phosphatase activity, are poorly understood. We have examined a neuronal type III RPTP, PTPRO; we find that PTPRO can form dimers in living cells, and that disulfide linkages in PTPROs intracellular domain likely regulate dimerization. Dimerization of PTPROs transmembrane and intracellular domains, achieved by ligand binding to a chimeric fusion protein, decreases activity toward artificial peptides and toward a putative substrate, tropomyosin-related kinase C (TrkC). Dephosphorylation of TrkC by PTPRO may be physiologically relevant, as it is efficient, and TrkC and PTPRO can be co-precipitated from transfected cells. Inhibition of PTPROs phosphatase activity by dimerization is interesting, as dimerization of a related RPTP, CD148/PTPRJ, increases activity. Thus, our results suggest a complex relationship between dimerization and activity in type III RPTPs.
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362
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Krishnamurthy D, Barrios AM. Profiling protein tyrosine phosphatase activity with mechanistic probes. Curr Opin Chem Biol 2009; 13:375-81. [PMID: 19716756 DOI: 10.1016/j.cbpa.2009.07.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 07/09/2009] [Accepted: 07/13/2009] [Indexed: 01/25/2023]
Abstract
The protein tyrosine phosphatases are a family of enzymes that play critical roles in regulating physiological processes including cellular signaling, growth, differentiation, and the immune response. As new roles emerge for these enzymes in human disease, interest in understanding their mechanism of regulation and function has increased correspondingly. The recent development of mechanism-based probes for phosphatase activity has paved the way for detailed studies of tyrosine phosphatase activity and regulation in both physiological and pathological cellular signaling.
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Affiliation(s)
- Divya Krishnamurthy
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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363
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Popov D. Vascular PTPs: current developments and challenges for exploitation in Type 2 diabetes-associated vascular dysfunction. Biochem Biophys Res Commun 2009; 389:1-4. [PMID: 19715673 DOI: 10.1016/j.bbrc.2009.08.110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 08/21/2009] [Indexed: 12/21/2022]
Abstract
Protein Tyrosine Phosphatases (PTPs) are important contributors to vascular cells normal function, by balancing signaling proteins activation exerted by phosphorylating kinases. Type 2 diabetes related insults, such as hyperglycemia, oxidative stress, and insulin resistance disturb the phosphorylation/dephosphorylation equilibrium towards an abnormal augmented phosphorylation of signaling proteins associated with changes in PTPs expression, enzymatic activity and interaction with cellular substrates. We briefly review here: (i) the new findings on receptor and non-receptor PTPs and their role in vascular cells, (ii) several data on oxidation and phosphorylation of these molecules in endothelial and smooth muscle cells, (iii) vascular PTPs intrinsic activity and dysregulation under the insults of diabetic milieu, and (iv) the potential use of PTPs and their inhibitors as therapeutic targets in Type 2 diabetes-associated vascular dysfunction.
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Affiliation(s)
- Doina Popov
- Institute of Cellular Biology and Pathology N. Simionescu, 050568 Bucharest, Romania.
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364
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Liu Y, Stanford SM, Jog SP, Fiorillo E, Orrú V, Comai L, Bottini N. Regulation of lymphoid tyrosine phosphatase activity: inhibition of the catalytic domain by the proximal interdomain. Biochemistry 2009; 48:7525-32. [PMID: 19586056 PMCID: PMC3113683 DOI: 10.1021/bi900332f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The lymphoid tyrosine phosphatase LYP, encoded by the PTPN22 gene, recently emerged as a major player and candidate drug target for human autoimmunity. The enzyme includes a classical N-terminal protein tyrosine phosphatase catalytic domain and a C-terminal PEST-enriched domain, separated by an approximately 300-amino acid interdomain. Little is known about the regulation of LYP. Herein, by analysis of serial truncation mutants of LYP, we show that the phosphatase activity is strongly inhibited by protein regions C-terminal to the catalytic domain. We mapped the minimal inhibitory region to the proximal portion of the interdomain. We show that the activity of LYP is inhibited by an intramolecular mechanism, whereby the proximal portion of the interdomain directly interacts with the catalytic domain and reduces its activity.
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Affiliation(s)
- Yingge Liu
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033
| | - Stephanie M. Stanford
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033
| | - Sonali P. Jog
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033
| | - Edoardo Fiorillo
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033
| | - Valeria Orrú
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033
| | - Lucio Comai
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033
| | - Nunzio Bottini
- Institute for Genetic Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033
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365
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Tsai SJ, Sen U, Zhao L, Greenleaf WB, Dasgupta J, Fiorillo E, Orrú V, Bottini N, Chen XS. Crystal structure of the human lymphoid tyrosine phosphatase catalytic domain: insights into redox regulation . Biochemistry 2009; 48:4838-45. [PMID: 19371084 DOI: 10.1021/bi900166y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lymphoid tyrosine phosphatase (LYP), encoded by the PTPN22 gene, recently emerged as an important risk factor and drug target for human autoimmunity. Here we solved the structure of the catalytic domain of LYP, which revealed noticeable differences with previously published structures. The active center with a semi-closed conformation binds a phosphate ion, which may represent an intermediate conformation after dephosphorylation of the substrate but before release of the phosphate product. The structure also revealed an unusual disulfide bond formed between the catalytic Cys and one of the two Cys residues nearby, which is not observed in previously determined structures. Our structural and mutagenesis data suggest that the disulfide bond may play a role in protecting the enzyme from irreversible oxidation. Surprisingly, we found that the two noncatalytic Cys around the active center exert an opposite yin-yang regulation on the catalytic Cys activity. These detailed structural and functional characterizations have provided new insights into autoregulatory mechanisms of LYP function.
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Affiliation(s)
- Sophia J Tsai
- Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
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366
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Sacco F, Tinti M, Palma A, Ferrari E, Nardozza AP, van Huijsduijnen RH, Takahashi T, Castagnoli L, Cesareni G. Tumor suppressor density-enhanced phosphatase-1 (DEP-1) inhibits the RAS pathway by direct dephosphorylation of ERK1/2 kinases. J Biol Chem 2009; 284:22048-22058. [PMID: 19494114 DOI: 10.1074/jbc.m109.002758] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Density-enhanced phosphatase-1 (DEP-1) is a trans-membrane receptor protein-tyrosine phosphatase that plays a recognized prominent role as a tumor suppressor. However, the mechanistic details underlying its function are poorly understood because its primary physiological substrate(s) have not been firmly established. To shed light on the mechanisms underlying the anti-proliferative role of this phosphatase, we set out to identify new DEP-1 substrates by a novel approach based on screening of high density peptide arrays. The results of the array experiment were combined with a bioinformatics filter to identify eight potential DEP-1 targets among the proteins annotated in the MAPK pathway. In this study we show that one of these potential targets, the ERK1/2, is indeed a direct DEP-1 substrate in vivo. Pulldown and in vitro dephosphorylation assays confirmed our prediction and demonstrated an overall specificity of DEP-1 in targeting the phosphorylated tyrosine 204 of ERK1/2. After epidermal growth factor stimulation, the phosphorylation of the activation loop of ERK1/2 can be modulated by changing the concentration of DEP-1, without affecting the activity of the upstream kinase MEK. In addition, we show that DEP-1 contains a KIM-like motif to recruit ERK1/2 proteins by a docking mechanism mediated by the common docking domain in ERK1/2. ERK proteins that are mutated in the conserved docking domain become insensitive to DEP-1 de-phosphorylation. Overall this study provides novel insights into the anti-proliferative role of this phosphatase and proposes a new mechanism that may also be relevant for the regulation of density-dependent growth inhibition.
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Affiliation(s)
- Francesca Sacco
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Michele Tinti
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Anita Palma
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Emanuela Ferrari
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Aurelio P Nardozza
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | | | - Takamune Takahashi
- Nephrology Division and Center for Vascular Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Luisa Castagnoli
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy; Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
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367
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Abstract
The large-scale structural biology projects that target human proteins focus predominantly on the catalytic domains of potential therapeutic targets and the domains of human proteins that mediate protein-protein and protein-small-molecule interactions. Their main scientific objective is to elucidate the molecular basis for specificity and selectivity of function within large protein families of therapeutic interest, such as kinases, phosphatases, and proteins involved in epigenetic regulation. Half of the unique human protein structures determined in the past three years derive from these initiatives.
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Affiliation(s)
- Aled Edwards
- Banting and Best Department of Medical Research, University of Toronto, Ontario M5G 1L6, Canada
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368
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Krishnan N, Jeong DG, Jung SK, Ryu SE, Xiao A, Allis CD, Kim SJ, Tonks NK. Dephosphorylation of the C-terminal tyrosyl residue of the DNA damage-related histone H2A.X is mediated by the protein phosphatase eyes absent. J Biol Chem 2009; 284:16066-16070. [PMID: 19351884 DOI: 10.1074/jbc.c900032200] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In mammalian cells, the DNA damage-related histone H2A variant H2A.X is characterized by a C-terminal tyrosyl residue, Tyr-142, which is phosphorylated by an atypical kinase, WSTF. The phosphorylation status of Tyr-142 in H2A.X has been shown to be an important regulator of the DNA damage response by controlling the formation of gammaH2A.X foci, which are platforms for recruiting molecules involved in DNA damage repair and signaling. In this work, we present evidence to support the identification of the Eyes Absent (EYA) phosphatases, protein-tyrosine phosphatases of the haloacid dehalogenase superfamily, as being responsible for dephosphorylating the C-terminal tyrosyl residue of histone H2A.X. We demonstrate that EYA2 and EYA3 displayed specificity for Tyr-142 of H2A.X in assays in vitro. Suppression of eya3 by RNA interference resulted in elevated basal phosphorylation and inhibited DNA damage-induced dephosphorylation of Tyr-142 of H2A.X in vivo. This study provides the first indication of a physiological substrate for the EYA phosphatases and suggests a novel role for these enzymes in regulation of the DNA damage response.
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Affiliation(s)
- Navasona Krishnan
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Dae Gwin Jeong
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoeun-Dong, Yuseong-Gu, Daejeon 305-333, Korea
| | - Suk-Kyeong Jung
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoeun-Dong, Yuseong-Gu, Daejeon 305-333, Korea
| | - Seong Eon Ryu
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoeun-Dong, Yuseong-Gu, Daejeon 305-333, Korea
| | - Andrew Xiao
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10065
| | - C David Allis
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10065
| | - Seung Jun Kim
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoeun-Dong, Yuseong-Gu, Daejeon 305-333, Korea.
| | - Nicholas K Tonks
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724.
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Gingras MC, Zhang YL, Kharitidi D, Barr AJ, Knapp S, Tremblay ML, Pause A. HD-PTP is a catalytically inactive tyrosine phosphatase due to a conserved divergence in its phosphatase domain. PLoS One 2009; 4:e5105. [PMID: 19340315 PMCID: PMC2661844 DOI: 10.1371/journal.pone.0005105] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 03/04/2009] [Indexed: 02/04/2023] Open
Abstract
Background The HD-PTP protein has been described as a tumor suppressor candidate and based on its amino acid sequence, categorized as a classical non-transmembrane protein tyrosine phosphatase (PTP). To date, no HD-PTP phosphorylated substrate has been identified and controversial results concerning its catalytic activity have been recently reported. Methodology and Results Here we report a rigorous enzymatic analysis demonstrating that the HD-PTP protein does not harbor tyrosine phosphatase or lipid phosphatase activity using the highly sensitive DiFMUP substrate and a panel of different phosphatidylinositol phosphates. We found that HD-PTP tyrosine phosphatase inactivity is caused by an evolutionary conserved amino acid divergence of a key residue located in the HD-PTP phosphatase domain since its back mutation is sufficient to restore the HD-PTP tyrosine phosphatase activity. Moreover, in agreement with a tumor suppressor activity, HD-PTP expression leads to colony growth reduction in human cancer cell lines, independently of its catalytic PTP activity status. Conclusion In summary, we demonstrate that HD-PTP is a catalytically inactive protein tyrosine phosphatase. As such, we identify one residue involved in its inactivation and show that its colony growth reduction activity is independent of its PTP activity status in human cancer cell lines.
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Affiliation(s)
- Marie-Claude Gingras
- Goodman Cancer Centre and Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Yu Ling Zhang
- Goodman Cancer Centre and Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Dmitri Kharitidi
- Goodman Cancer Centre and Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Alastair J. Barr
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Michel L. Tremblay
- Goodman Cancer Centre and Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Arnim Pause
- Goodman Cancer Centre and Department of Biochemistry, McGill University, Montréal, Québec, Canada
- * E-mail:
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Research highlights. Nat Chem Biol 2009. [DOI: 10.1038/nchembio0309-148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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