1
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Gallenga CE, Lonardi M, Pacetti S, Violanti SS, Tassinari P, Di Virgilio F, Tognon M, Perri P. Molecular Mechanisms Related to Oxidative Stress in Retinitis Pigmentosa. Antioxidants (Basel) 2021; 10:antiox10060848. [PMID: 34073310 PMCID: PMC8229325 DOI: 10.3390/antiox10060848] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/17/2022] Open
Abstract
Retinitis pigmentosa (RP) is an inherited retinopathy. Nevertheless, non-genetic biological factors play a central role in its pathogenesis and progression, including inflammation, autophagy and oxidative stress. The retina is particularly affected by oxidative stress due to its high metabolic rate and oxygen consumption as well as photosensitizer molecules inside the photoreceptors being constantly subjected to light/oxidative stress, which induces accumulation of ROS in RPE, caused by damaged photoreceptor’s daily recycling. Oxidative DNA damage is a key regulator of microglial activation and photoreceptor degeneration in RP, as well as mutations in endogenous antioxidant pathways involved in DNA repair, oxidative stress protection and activation of antioxidant enzymes (MUTYH, CERKL and GLO1 genes, respectively). Moreover, exposure to oxidative stress alters the expression of micro-RNA (miRNAs) and of long non-codingRNA (lncRNAs), which might be implicated in RP etiopathogenesis and progression, modifying gene expression and cellular response to oxidative stress. The upregulation of the P2X7 receptor (P2X7R) also seems to be involved, causing pro-inflammatory cytokines and ROS release by macrophages and microglia, contributing to neuroinflammatory and neurodegenerative progression in RP. The multiple pathways analysed demonstrate that oxidative microglial activation may trigger the vicious cycle of non-resolved neuroinflammation and degeneration, suggesting that microglia may be a key therapy target of oxidative stress in RP.
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Affiliation(s)
- Carla Enrica Gallenga
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (C.E.G.); (F.D.V.); (M.T.)
| | - Maria Lonardi
- Department of Specialized Surgery, Section of Ophthalmology, Sant’Anna University Hospital, 44121 Ferrara, Italy; (M.L.); (S.P.); (P.T.)
| | - Sofia Pacetti
- Department of Specialized Surgery, Section of Ophthalmology, Sant’Anna University Hospital, 44121 Ferrara, Italy; (M.L.); (S.P.); (P.T.)
| | - Sara Silvia Violanti
- Department of Head and Neck, Section of Ophthalmology, San Paolo Hospital, 17100 Savona, Italy;
| | - Paolo Tassinari
- Department of Specialized Surgery, Section of Ophthalmology, Sant’Anna University Hospital, 44121 Ferrara, Italy; (M.L.); (S.P.); (P.T.)
| | - Francesco Di Virgilio
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (C.E.G.); (F.D.V.); (M.T.)
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (C.E.G.); (F.D.V.); (M.T.)
| | - Paolo Perri
- Department of Neuroscience and Rehabilitation, Section of Ophthalmology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence:
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2
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Tong M, Liu P, Sun W, Liu J, Fan N, Wang X, Zhang Z, Song X, Lv C, Wang Y. Molecular dynamics simulation studies on the specific regulation of PTPN18 to the HER2 phospho-peptides. J Mol Recognit 2021; 34:e2890. [PMID: 33620127 DOI: 10.1002/jmr.2890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 11/09/2022]
Abstract
The specific regulation of PTPN18 protein to three HER2 phospho-peptides has been studied by molecular dynamics simulations and free energy calculations. The results revealed that the three HER2 phospho-peptides binding to the PTPN18 catalytic domain is energetically favorable due to substrate specificity of PTPN18, and moreover, the PTPN18 protein have significantly higher affinity to pY1248 peptide (-45.22 kcal/mol) than that of pY1112 (-25.3 kcal/mol) and pY1196 (-31.86 kcal/mol) peptides. Further, the binding of HER2 phospho-peptides to PTPN18 have also caused the closure of WPD-loop with the decrease of the centroid distances between the P-loop and the WPD loop. The WPD-loop closure of PTPN18 relates directly to the new hydrogen bond and hydrophobic interaction formations between the residues Tyr62, Asp64, Val65, Ala231, Arg235, and Ala273 in PTPN18 and Tyr(PO3) in the HER2 phospho-peptides, which suggests that these key residues would contribute to the specific regulation of PTPN18 to the substrates. The correlation analysis revealed the allosteric communication networks from the pY binding loop to the WPD loop through the structural change and the residue interactions in PTPN18. These results will be helpful to understand the specific regulation through the allosteric communication network in the PTPN18 catalytic domain.
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Affiliation(s)
- Mingqiong Tong
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Peng Liu
- The Office of Academic Affairs, Dezhou University, Dezhou, China
| | - Wan Sun
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Jing Liu
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Na Fan
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Xiaoyue Wang
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Zhongyu Zhang
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Xinfeng Song
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Chao Lv
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Yan Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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3
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Donato L, Scimone C, Alibrandi S, Nicocia G, Rinaldi C, Sidoti A, D’Angelo R. Discovery of GLO1 New Related Genes and Pathways by RNA-Seq on A2E-Stressed Retinal Epithelial Cells Could Improve Knowledge on Retinitis Pigmentosa. Antioxidants (Basel) 2020; 9:E416. [PMID: 32413970 PMCID: PMC7278727 DOI: 10.3390/antiox9050416] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/02/2020] [Accepted: 05/10/2020] [Indexed: 12/15/2022] Open
Abstract
Endogenous antioxidants protect cells from reactive oxygen species (ROS)-related deleterious effects, and an imbalance in the oxidant/antioxidant systems generates oxidative stress. Glyoxalase 1 (GLO1) is a ubiquitous cellular enzyme involved in detoxification of methylglyoxal (MG), a cytotoxic byproduct of glycolysis whose excess can produce oxidative stress. In retinitis pigmentosa, one of the most diffuse cause of blindness, oxidative damage leads to photoreceptor death. To clarify the role of GLO1 in retinitis pigmentosa onset and progression, we treated human retinal pigment epithelium cells by the oxidant agent A2E. Transcriptome profiles between treated and untreated cells were performed by RNA-Seq, considering two time points (3 and 6 h), after the basal one. The exposure to A2E highlighted significant expression differences and splicing events in 370 GLO1 first-neighbor genes, and 23 of them emerged from pathway clustered analysis as main candidates to be associated with retinitis pigmentosa. Such a hypothesis was corroborated by the involvement of previously analyzed genes in specific cellular activities related to oxidative stress, such as glyoxylate and dicarboxylate metabolism, glycolysis, axo-dendritic transport, lipoprotein activity and metabolism, SUMOylation and retrograde transport at the trans-Golgi network. Our findings could be the starting point to explore unclear molecular mechanisms involved in retinitis pigmentosa etiopathogenesis.
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Affiliation(s)
- Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (C.S.); (S.A.); (C.R.); (R.D.)
- Department of Biomolecular strategies, genetics and avant-garde therapies, I.E.ME.S.T., 90139 Palermo, Italy
| | - Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (C.S.); (S.A.); (C.R.); (R.D.)
- Department of Biomolecular strategies, genetics and avant-garde therapies, I.E.ME.S.T., 90139 Palermo, Italy
| | - Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (C.S.); (S.A.); (C.R.); (R.D.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98125 Messina, Italy
| | - Giacomo Nicocia
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy;
| | - Carmela Rinaldi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (C.S.); (S.A.); (C.R.); (R.D.)
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (C.S.); (S.A.); (C.R.); (R.D.)
- Department of Biomolecular strategies, genetics and avant-garde therapies, I.E.ME.S.T., 90139 Palermo, Italy
| | - Rosalia D’Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98125 Messina, Italy; (C.S.); (S.A.); (C.R.); (R.D.)
- Department of Biomolecular strategies, genetics and avant-garde therapies, I.E.ME.S.T., 90139 Palermo, Italy
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4
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Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. eLife 2018; 7:36307. [PMID: 29877794 PMCID: PMC6039181 DOI: 10.7554/elife.36307] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/04/2018] [Indexed: 12/28/2022] Open
Abstract
Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here, we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function. Proteins perform many important jobs in each of the cells in our bodies, such as transporting other molecules and helping chemical reactions to occur. The part of the protein directly involved in these tasks is called the active site. Other areas of the protein can communicate with the active site to switch the protein on or off. This method of control is known as allostery. Switching proteins on and off could help us to develop treatments for certain diseases. For example, a protein called PTP1B reduces how well cells can respond to insulin. Switching this protein off could therefore help to treat diabetes. However, much like it’s hard to guess how a light switch is wired to a light bulb without seeing behind the walls, it is hard to predict which remote areas of a protein are ‘wired’ to the active site. Keedy, Hill et al. have now used two complementary methods to examine the structure of PTP1B and find new allosteric sites. The first method captured a series of X-ray images from crystallized molecules of the protein held at different temperatures. This revealed areas of PTP1B that can move like windshield wipers to communicate with each other. The second method soaked PTP1B crystals in trays with hundreds of drug-sized molecules and assessed which sites on the protein the molecules bound to. The molecules generally bound to just a few sites of the protein. Further tests on one of these sites showed that it can communicate with the active site to turn the protein on or off. Further work will be needed to develop drugs that could treat diabetes by binding to the newly identified allosteric sites in PTP1B. More generally, the methods developed by Keedy, Hill et al. could be used to study allostery in other important proteins.
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Affiliation(s)
- Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Zachary B Hill
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Justin T Biel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Emily Kang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - T Justin Rettenmaier
- Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | | | - Nicholas M Pearce
- Crystal and Structural Chemistry Group, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Frank von Delft
- Diamond Light Source, Didcot, United Kingdom.,Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom.,Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
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5
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Xu S, Wang T, Yang Z, Li Y, Li W, Wang T, Wang S, Jia L, Zhang S, Li S. miR-26a desensitizes non-small cell lung cancer cells to tyrosine kinase inhibitors by targeting PTPN13. Oncotarget 2018; 7:45687-45701. [PMID: 27285768 PMCID: PMC5216753 DOI: 10.18632/oncotarget.9920] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/23/2016] [Indexed: 12/24/2022] Open
Abstract
Epidermal growth factor receptor (EGFR)-targeted tyrosine kinase inhibitors (TKIs) have emerged as first-line drugs for non-small cell lung cancers (NSCLCs). However, the resistance to TKIs represents the key limitation for their therapeutic efficacy. We found that miR-26a was upregulated in gefitinib-refractory NSCLCs; miR-26a is downstream of EGFR signaling and directly targets and silences protein tyrosine phosphatase non-receptor type 13 (PTPN13) to maintain the activation of Src, a dephosphorylation substrate of PTPN13, thus reinforcing EGFR pathway in a regulatory circuit. miR-26a inhibition significantly improved NSCLC responses to gefitinib. These data revealed a novel mechanism of NSCLC resistance to TKI treatment.
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Affiliation(s)
- Shudi Xu
- Department of Respiratory Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Department of Respiratory Medicine, 9th Hospital of Xi'an, Xi'an, China
| | - Tao Wang
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Zhiwei Yang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an, China
| | - Ying Li
- Department of Respiratory Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Department of Respiratory Medicine, Shaanxi Provincial Second People's Hospital, Xi'an, China
| | - Weijie Li
- Department of Respiratory Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Ting Wang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Shan Wang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Lintao Jia
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Shengli Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an, China
| | - Shengqing Li
- Department of Respiratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
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6
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Bishop AC. A missense methionine mutation augments catalytic activity but reduces thermal stability in two protein tyrosine phosphatases. Biochem Biophys Res Commun 2016; 481:153-158. [PMID: 27816449 PMCID: PMC5118098 DOI: 10.1016/j.bbrc.2016.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/01/2016] [Indexed: 11/23/2022]
Abstract
Recent data sets that catalog the missense mutations in thousands of human genomes have revealed a vast and largely unexplored world of non-canonical protein sequences that are expressed in humans. The functional consequences of most human missense mutations, however, are unknown, and the accuracy with which their effects can be predicted by computational algorithms remains unclear. Among humans of European descent, the most common missense mutation in the catalytic domain of SH2-containing protein tyrosine phosphatase 1 (SHP-1) converts the enzyme's canonical valine 451 to methionine (V451M). The V451M mutation lies in a conserved motif adjacent to the protein tyrosine phosphatase (PTP) consensus sequence and is predicted to compromise catalytic function. In this study it is shown that, counter to prediction, V451M SHP-1 possesses increased catalytic activity as compared to the wild-type enzyme. Additionally, a PTP-wide search of missense-mutation data revealed a variant of one other PTP, Fas-associated PTP (FAP-1), that contains a methionine mutation at the position corresponding to 451 of SHP-1 (T2406M FAP-1). It is shown here that the T2406M mutation increases FAP-1's PTP activity, to a degree that is comparable to the activation deriving from the V451M mutation in SHP-1. Although the two non-canonical methionine residues confer increased activity at moderate temperatures, both V451M SHP-1 and T2406M FAP-1 are less thermally stable than their canonical counterparts, as demonstrated by the mutants' strongly reduced activities at high temperatures. These results highlight the challenges in predicting the functional consequences of missense mutations, which can differ under varying conditions, and suggest that, with regard to position 451/2406, canonical PTP domains have "chosen" stability over optimized activity during the course of evolution.
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Affiliation(s)
- Anthony C Bishop
- Amherst College, Department of Chemistry, Amherst, MA 01002, USA.
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7
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Lee SO, Lee MK, Ku B, Bae KH, Lee SC, Lim HM, Kim SJ, Chi SW. High-resolution crystal structure of the PDZ1 domain of human protein tyrosine phosphatase PTP-Bas. Biochem Biophys Res Commun 2016; 478:1205-10. [DOI: 10.1016/j.bbrc.2016.08.095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/16/2016] [Indexed: 10/21/2022]
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8
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Li H, Yang F, Liu C, Xiao P, Xu Y, Liang Z, Liu C, Wang H, Wang W, Zheng W, Zhang W, Ma X, He D, Song X, Cui F, Xu Z, Yi F, Sun JP, Yu X. Crystal Structure and Substrate Specificity of PTPN12. Cell Rep 2016; 15:1345-58. [DOI: 10.1016/j.celrep.2016.04.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 01/27/2016] [Accepted: 03/29/2016] [Indexed: 01/21/2023] Open
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9
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Chio CM, Yu X, Bishop AC. Rational design of allosteric-inhibition sites in classical protein tyrosine phosphatases. Bioorg Med Chem 2015; 23:2828-38. [PMID: 25828055 PMCID: PMC4451255 DOI: 10.1016/j.bmc.2015.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/05/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022]
Abstract
Protein tyrosine phosphatases (PTPs), which catalyze the dephosphorylation of phosphotyrosine in protein substrates, are critical regulators of metazoan cell signaling and have emerged as potential drug targets for a range of human diseases. Strategies for chemically targeting the function of individual PTPs selectively could serve to elucidate the signaling roles of these enzymes and would potentially expedite validation of the therapeutic promise of PTP inhibitors. Here we report a novel strategy for the design of non-natural allosteric-inhibition sites in PTPs; these sites, which can be introduced into target PTPs through protein engineering, serve to sensitize target PTPs to potent and selective inhibition by a biarsenical small molecule. Building on the recent discovery of a naturally occurring cryptic allosteric site in wild-type Src-homology-2 domain containing PTP (Shp2) that can be targeted by biarsenical compounds, we hypothesized that Shp2's unusual sensitivity to biarsenicals could be strengthened through rational design and that the Shp2-specific site could serve as a blueprint for the introduction of non-natural inhibitor sensitivity in other PTPs. Indeed, we show here that the strategic introduction of a cysteine residue at a position removed from the Shp2 active site can serve to increase the potency and selectivity of the interaction between Shp2's allosteric site and the biarsenical inhibitor. Moreover, we find that 'Shp2-like' allosteric sites can be installed de novo in PTP enzymes that do not possess naturally occurring sensitivity to biarsenical compounds. Using primary-sequence alignments to guide our enzyme engineering, we have successfully introduced allosteric-inhibition sites in four classical PTPs-PTP1B, PTPH-1, FAP-1, and HePTP-from four different PTP subfamilies, suggesting that our sensitization approach can likely be applied widely across the classical PTP family to generate biarsenical-responsive PTPs.
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Affiliation(s)
- Cynthia M Chio
- Amherst College, Department of Chemistry, Amherst, MA 01002, United States
| | - Xiaoling Yu
- Amherst College, Department of Chemistry, Amherst, MA 01002, United States
| | - Anthony C Bishop
- Amherst College, Department of Chemistry, Amherst, MA 01002, United States.
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10
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Chen KE, Li MY, Chou CC, Ho MR, Chen GC, Meng TC, Wang AJ. Substrate Specificity and Plasticity of FERM-Containing Protein Tyrosine Phosphatases. Structure 2015; 23:653-64. [DOI: 10.1016/j.str.2015.01.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 01/18/2015] [Accepted: 01/24/2015] [Indexed: 10/23/2022]
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11
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Identification of a novel stress regulated FERM domain containing cytosolic protein having PTP activity in Setaria cervi, a bovine filarial parasite. Biochem Biophys Res Commun 2015; 458:194-200. [PMID: 25645020 DOI: 10.1016/j.bbrc.2015.01.100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 01/21/2015] [Indexed: 11/23/2022]
Abstract
A 67 kDa cytosolic FERM domain containing protein having significant protein tyrosine phosphatases activity (PTPL) has been purified to homogeneity from Setaria cervi, a bovine filarial parasite. The MALDI-MS/MS analysis of the purified protein revealed 16 peptide peaks showing nearest match to Brugia malayi Moesin/ezrin/radixin homolog 1 protein and one peptide showing significant similarity with a region lying in the catalytic domain of human PTPD1. PTPL showed significant cross reactivity with the human PTP1B antibody and colocalize with actin in the coelomyrian cells of hypodermis in the parasite. PTPL was stress regulated as it showed marked decrease in the expression when exposed to Aspirin, an antifilarial drug and Phenylarsine Oxide, PTP inhibitor.
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12
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He RJ, Yu ZH, Zhang RY, Zhang ZY. Protein tyrosine phosphatases as potential therapeutic targets. Acta Pharmacol Sin 2014; 35:1227-46. [PMID: 25220640 DOI: 10.1038/aps.2014.80] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 07/31/2014] [Indexed: 12/17/2022] Open
Abstract
Protein tyrosine phosphorylation is a key regulatory process in virtually all aspects of cellular functions. Dysregulation of protein tyrosine phosphorylation is a major cause of human diseases, such as cancers, diabetes, autoimmune disorders, and neurological diseases. Indeed, protein tyrosine phosphorylation-mediated signaling events offer ample therapeutic targets, and drug discovery efforts to date have brought over two dozen kinase inhibitors to the clinic. Accordingly, protein tyrosine phosphatases (PTPs) are considered next-generation drug targets. For instance, PTP1B is a well-known targets of type 2 diabetes and obesity, and recent studies indicate that it is also a promising target for breast cancer. SHP2 is a bona-fide oncoprotein, mutations of which cause juvenile myelomonocytic leukemia, acute myeloid leukemia, and solid tumors. In addition, LYP is strongly associated with type 1 diabetes and many other autoimmune diseases. This review summarizes recent findings on several highly recognized PTP family drug targets, including PTP1B, Src homology phosphotyrosyl phosphatase 2(SHP2), lymphoid-specific tyrosine phosphatase (LYP), CD45, Fas associated phosphatase-1 (FAP-1), striatal enriched tyrosine phosphatases (STEP), mitogen-activated protein kinase/dual-specificity phosphatase 1 (MKP-1), phosphatases of regenerating liver-1 (PRL), low molecular weight PTPs (LMWPTP), and CDC25. Given that there are over 100 family members, we hope this review will serve as a road map for innovative drug discovery targeting PTPs.
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13
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Role of TAPP1 and TAPP2 adaptor binding to PtdIns(3,4)P2 in regulating insulin sensitivity defined by knock-in analysis. Biochem J 2011; 434:265-74. [PMID: 21204784 DOI: 10.1042/bj20102012] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Insulin sensitivity is critically dependent on the activity of PI3K (phosphoinositide 3-kinase) and generation of the PtdIns(3,4,5)P(3) second messenger. PtdIns(3,4,5)P(3) can be broken down to PtdIns(3,4)P(2) through the action of the SHIPs (Src-homology-2-domain-containing inositol phosphatases). As PtdIns(3,4)P(2) levels peak after those of PtdIns(3,4,5)P(3), it has been proposed that PtdIns(3,4)P(2) controls a negative-feedback loop that down-regulates the insulin and PI3K network. Previously, we identified two related adaptor proteins termed TAPP [tandem PH (pleckstrin homology)-domain-containing protein] 1 and TAPP2 that specifically bind to PtdIns(3,4)P(2) through their C-terminal PH domain. To determine whether TAPP1 and TAPP2 play a role in regulating insulin sensitivity, we generated knock-in mice that express normal endogenous levels of mutant TAPP1 and TAPP2 that are incapable of binding PtdIns(3,4)P(2). These homozygous TAPP1(R211L/R211L) TAPP2(R218L/R218L) double knock-in mice are viable and exhibit significantly enhanced activation of Akt, a key downstream mediator of insulin signalling. Consistent with increased PI3K and Akt activity, the double knock-in mice display enhanced whole body insulin sensitivity and disposal of glucose uptake into muscle tissues. We also generated wild-type and double TAPP1(R211L/R211L) TAPP2(R218L/R218L) knock-in embryonic fibroblasts and found that insulin triggered enhanced production of PtdIns(3,4,5)P(3) and Akt activity in the double knock-in fibroblasts. These observations provide the first genetic evidence to support the notion that binding of TAPP1 and TAPP2 adap-tors to PtdIns(3,4)P(2) function as negative regulators of the insulin and PI3K signalling pathways.
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14
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Olmez EO, Alakent B. Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B. J Biomol Struct Dyn 2011; 28:675-93. [DOI: 10.1080/07391102.2011.10508599] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Critton DA, Tautz L, Page R. Visualizing active-site dynamics in single crystals of HePTP: opening of the WPD loop involves coordinated movement of the E loop. J Mol Biol 2010; 405:619-29. [PMID: 21094165 DOI: 10.1016/j.jmb.2010.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 11/09/2010] [Accepted: 11/10/2010] [Indexed: 10/18/2022]
Abstract
Phosphotyrosine hydrolysis by protein tyrosine phosphatases (PTPs) involves substrate binding by the PTP loop and closure over the active site by the WPD loop. The E loop, located immediately adjacent to the PTP and WPD loops, is conserved among human PTPs in both sequence and structure, yet the role of this loop in substrate binding and catalysis is comparatively unexplored. Hematopoietic PTP (HePTP) is a member of the kinase interaction motif (KIM) PTP family. Compared to other PTPs, KIM-PTPs have E loops that are unique in both sequence and structure. In order to understand the role of the E loop in the transition between the closed state and the open state of HePTP, we identified a novel crystal form of HePTP that allowed the closed-state-to-open-state transition to be observed within a single crystal form. These structures, which include the first structure of the HePTP open state, show that the WPD loop adopts an 'atypically open' conformation and, importantly, that ligands can be exchanged at the active site, which is critical for HePTP inhibitor development. These structures also show that tetrahedral oxyanions bind at a novel secondary site and function to coordinate the PTP, WPD, and E loops. Finally, using both structural and kinetic data, we reveal a novel role for E-loop residue Lys182 in enhancing HePTP catalytic activity through its interaction with Asp236 of the WPD loop, providing the first evidence for the coordinated dynamics of the WPD and E loops in the catalytic cycle, which, as we show, is relevant to multiple PTP families.
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Affiliation(s)
- David A Critton
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
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16
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Hoover AC, Strand GL, Nowicki PN, Anderson ME, Vermeer PD, Klingelhutz AJ, Bossler AD, Pottala JV, Hendriks WJAJ, Lee JH. Impaired PTPN13 phosphatase activity in spontaneous or HPV-induced squamous cell carcinomas potentiates oncogene signaling through the MAP kinase pathway. Oncogene 2009; 28:3960-70. [PMID: 19734941 PMCID: PMC2785129 DOI: 10.1038/onc.2009.251] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Human papillomaviruses (HPVs) are a causative factor in over 90% of cervical and 25% of head and neck squamous cell carcinomas (HNSCCs). The C terminus of the high-risk HPV 16 E6 oncoprotein physically associates with and degrades a non-receptor protein tyrosine phosphatase (PTPN13), and PTPN13 loss synergizes with H-Ras(V12) or ErbB2 for invasive growth in vivo. Oral keratinocytes that have lost PTPN13 and express H-Ras(V12) or ErbB2 show enhanced Ras/RAF/MEK/Erk signaling. In co-transfection studies, wild-type PTPN13 inhibited Ras/RAF/MEK/Erk signaling in HEK 293 cells that overexpress ErbB2, EGFR or H-Ras(V12), whereas an enzymatically inactive PTPN13 did not. Twenty percent of HPV-negative HNSCCs had PTPN13 phosphatase mutations that did not inhibit Ras/RAF/MEK/Erk signaling. Inhibition of Ras/RAF/MEK/Erk signaling using MEK inhibitor U0126 blocked anchorage-independent growth in cells lacking PTPN13. These findings show that PTPN13 phosphatase activity has a physiologically significant role in regulating MAP kinase signaling.
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Affiliation(s)
- A C Hoover
- Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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17
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Mita Y, Yasuda Y, Sakai A, Yamamoto H, Toyooka S, Gunduz M, Tanabe S, Naomoto Y, Ouchida M, Shimizu K. Missense polymorphisms of PTPRJ and PTPN13 genes affect susceptibility to a variety of human cancers. J Cancer Res Clin Oncol 2009; 136:249-59. [DOI: 10.1007/s00432-009-0656-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2009] [Accepted: 07/28/2009] [Indexed: 12/28/2022]
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18
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Barr AJ, Ugochukwu E, Lee WH, King ON, Filippakopoulos P, Alfano I, Savitsky P, Burgess-Brown NA, Müller S, Knapp S. Large-scale structural analysis of the classical human protein tyrosine phosphatome. Cell 2009; 136:352-63. [PMID: 19167335 PMCID: PMC2638020 DOI: 10.1016/j.cell.2008.11.038] [Citation(s) in RCA: 358] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 09/15/2008] [Accepted: 11/20/2008] [Indexed: 02/05/2023]
Abstract
Protein tyrosine phosphatases (PTPs) play a critical role in regulating cellular functions by selectively dephosphorylating their substrates. Here we present 22 human PTP crystal structures that, together with prior structural knowledge, enable a comprehensive analysis of the classical PTP family. Despite their largely conserved fold, surface properties of PTPs are strikingly diverse. A potential secondary substrate-binding pocket is frequently found in phosphatases, and this has implications for both substrate recognition and development of selective inhibitors. Structural comparison identified four diverse catalytic loop (WPD) conformations and suggested a mechanism for loop closure. Enzymatic assays revealed vast differences in PTP catalytic activity and identified PTPD1, PTPD2, and HDPTP as catalytically inert protein phosphatases. We propose a “head-to-toe” dimerization model for RPTPγ/ζ that is distinct from the “inhibitory wedge” model and that provides a molecular basis for inhibitory regulation. This phosphatome resource gives an expanded insight into intrafamily PTP diversity, catalytic activity, substrate recognition, and autoregulatory self-association.
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Affiliation(s)
- Alastair J. Barr
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
- Corresponding author
| | - Emilie Ugochukwu
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Wen Hwa Lee
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Oliver N.F. King
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Panagis Filippakopoulos
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Ivan Alfano
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Pavel Savitsky
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Nicola A. Burgess-Brown
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Susanne Müller
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Stefan Knapp
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
- University of Oxford, Department of Clinical Pharmacology, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
- Corresponding author
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19
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Abstract
Protein tyrosine phosphatase, PTPL1, (also known as PTPN13, FAP-1, PTP-BAS, PTP1E) is a non-receptor type PTP and, at 270 kDa, is the largest phosphatase within this group. In addition to the well-conserved PTP domain, PTPL1 contains at least 7 putative macromolecular interaction domains. This structural complexity indicates that PTPL1 may modulate diverse cellular functions, perhaps exerting both positive and negative effects. In accordance with this idea, while certain studies suggest that PTPL1 can act as a tumor-promoting gene other experimental studies have suggested that PTPL1 may function as a tumor suppressor. The role of PTPL1 in the cancer cell is therefore likely to be both complex and context dependent with possible roles including the modulation of growth, stress-response, and cytoskeletal remodeling pathways. Understanding the nature of molecular complexes containing PTPL1, its interaction partners, substrates, regulation and subcellular localization are key to unraveling the complex personality of this protein phosphatase.
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20
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Grundner C, Ng HL, Alber T. Mycobacterium tuberculosis protein tyrosine phosphatase PtpB structure reveals a diverged fold and a buried active site. Structure 2008; 13:1625-34. [PMID: 16271885 DOI: 10.1016/j.str.2005.07.017] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Revised: 07/18/2005] [Accepted: 07/23/2005] [Indexed: 01/06/2023]
Abstract
Intracellular pathogenic bacteria manipulate host signal transduction pathways to facilitate infection. Mycobacterium tuberculosis protein tyrosine phosphatases (PTPs) PtpA and PtpB are thought to be secreted into host cells and interfere with unidentified signals. To illuminate the mechanisms of regulation and substrate recognition, we determined the 1.7 A resolution crystal structure of PtpB in complex with the product phosphate. The protein adopts a simplified PTP fold, which combines features of the conventional PTPs and dual-specificity phosphatases. PtpB shows two unusual elaborations--a disordered, acidic loop and a flexible, two-helix lid that covers the active site--that are specific to mycobacterial orthologs. Biochemical studies suggest that substrate mimicry in the lid may protect the phosphatase from oxidative inactivation. The insertion and deletion of large structural elements in PtpB suggest that, outside the active site module, the PTP family is under unusual selective pressure that promotes changes in overall structure.
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Affiliation(s)
- Christoph Grundner
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
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21
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Holmes CP, Macher N, Grove JR, Jang L, Irvine JD. Designing better coumarin-based fluorogenic substrates for PTP1B. Bioorg Med Chem Lett 2008; 18:3382-5. [DOI: 10.1016/j.bmcl.2008.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 04/05/2008] [Accepted: 04/10/2008] [Indexed: 10/22/2022]
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22
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Tabernero L, Aricescu AR, Jones EY, Szedlacsek SE. Protein tyrosine phosphatases: structure-function relationships. FEBS J 2008; 275:867-82. [PMID: 18298793 DOI: 10.1111/j.1742-4658.2008.06251.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structural analysis of protein tyrosine phosphatases (PTPs) has expanded considerably in the last several years, producing more than 200 structures in this class of enzymes (from 35 different proteins and their complexes with ligands). The small-medium size of the catalytic domain of approximately 280 residues plus a very compact fold makes it amenable to cloning and overexpression in bacterial systems thus facilitating crystallographic analysis. The low molecular weight PTPs being even smaller, approximately 150 residues, are also perfect targets for NMR analysis. The availability of different structures and complexes of PTPs with substrates and inhibitors has provided a wealth of information with profound effects in the way we understand their biological functions. Developments in mammalian expression technology recently led to the first crystal structure of a receptor-like PTP extracellular region. Altogether, the PTP structural work significantly advanced our knowledge regarding the architecture, regulation and substrate specificity of these enzymes. In this review, we compile the most prominent structural traits that characterize PTPs and their complexes with ligands. We discuss how the data can be used to design further functional experiments and as a basis for drug design given that many PTPs are now considered strategic therapeutic targets for human diseases such as diabetes and cancer.
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23
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The PDZ binding motif of human papillomavirus type 16 E6 induces PTPN13 loss, which allows anchorage-independent growth and synergizes with ras for invasive growth. J Virol 2007; 82:2493-500. [PMID: 18160445 DOI: 10.1128/jvi.02188-07] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human papillomavirus (HPV) oncogene E6 has been shown to perform multiple functions (p53 degradation, telomerase activation, etc.) that play a role in oncogenic transformation. Beyond known E6 functions, an undefined mechanism that allows cellular invasion requires the E6 PDZ binding motif (PDZBM). Here, we show that HPV type 16 (HPV16) E6 interacts with and induces loss of a protein tyrosine phosphatase (PTPN13) in a PDZBM-dependent manner. PTPN13 loss induced either by the presence of E6 or by a short hairpin RNA strategy allows for anchorage-independent growth (AIG) and synergy with a known oncogene, Ras(v12), resulting in invasive growth in vivo. Restoring PTPN13 expression reverses AIG in cells lacking PTPN13. A genomic analysis of colorectal carcinoma has identified an association between PTPN13 loss-of-function mutations and aberrant Ras signaling. Our findings support this correlation and provide methods for further evaluation of the mechanisms by which PTPN13 loss/Ras expression leads to invasive growth, the results of which will be important for treatment of HPV-related and non-HPV cancer.
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24
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Dromard M, Bompard G, Glondu-Lassis M, Puech C, Chalbos D, Freiss G. The putative tumor suppressor gene PTPN13/PTPL1 induces apoptosis through insulin receptor substrate-1 dephosphorylation. Cancer Res 2007; 67:6806-13. [PMID: 17638892 DOI: 10.1158/0008-5472.can-07-0513] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The protein tyrosine phosphatase (PTP) PTPL1/PTPN13 is a candidate tumor suppressor gene. Indeed, PTPL1 activity has been reported recently to be decreased through somatic mutations, allelic loss, or promoter methylation in some tumors. We showed previously that its expression was necessary for inhibition of Akt activation and induction of apoptosis by antiestrogens in breast cancer cells. Implications of the phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathway in cancer progression are now well established, and our study was therefore designed to define whether PTPL1 is sufficient to inhibit this pathway and, if so, to identify a direct substrate of this PTP, which may trigger a proapoptotic effect. We first show by complementary approaches that PTPL1 specifically dephosphorylates insulin receptor substrate-1 (IRS-1) in vitro and in cellulo. Next, our experiments using a dominant-negative mutant and RNA interference confirm the crucial role of PTPL1 in IRS-1 dephosphorylation. Finally, we report that PTPL1 expression is sufficient to block the IRS-1/PI3K/Akt signaling pathway, to inhibit the insulin-like growth factor-I effect on cell survival, and to induce apoptosis. Altogether, these data provide the first evidence for a direct positive role of the putative tumor suppressor gene PTPL1/PTPN13 on apoptosis and identify its target in the IRS-1/PI3K/Akt signaling pathway.
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Affiliation(s)
- Mathilde Dromard
- INSERM U826, Contrôle de la Progression des Cancers Hormono-Dépendants, Centre de Recherche en Cancérologie, Universite Montpellier I, CRLC Val d'Aurelle-Paul Lamarque, 34298 Montpellier, France
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25
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Ross SH, Lindsay Y, Safrany ST, Lorenzo O, Villa F, Toth R, Clague MJ, Downes CP, Leslie NR. Differential redox regulation within the PTP superfamily. Cell Signal 2007; 19:1521-30. [PMID: 17346927 DOI: 10.1016/j.cellsig.2007.01.026] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Revised: 01/26/2007] [Accepted: 01/26/2007] [Indexed: 11/18/2022]
Abstract
The Protein Tyrosine Phosphatase (PTP) family comprises a large and diverse group of enzymes, regulating a range of biological processes through de-phosphorylation of many proteins and lipids. These enzymes share a catalytic mechanism that requires a reduced and reactive cysteine nucleophile, making them potentially sensitive to inactivation and regulation by oxidation. Analysis of ten PTPs identified substantial differences in the sensitivity of these enzymes to oxidation in vitro. More detailed experiments confirmed the following rank order of sensitivity: PTEN and Sac1>PTPL1/FAP-1>>myotubularins. When the apparent sensitivity to oxidation of these PTPs in cells treated with hydrogen peroxide was analysed, this correlated well with the observed sensitivities to oxidation in vitro. These data suggested that different PTPs may fall into at least three different classes with respect to mechanisms of cellular redox regulation. 1. PTEN and Sac1 were readily and reversibly oxidised in vitro and in cells treated with hydrogen peroxide 2. PTPL1 appeared to be resistant to oxidation in cells, correlating with its sensitivity to reduction by glutathione in vitro 3. The myotubularin family of lipid phosphatases was almost completely resistant to oxidation in vitro and in cells. Our results show that sensitivity to reversible oxidation is not a necessary characteristic of the PTPs and imply that such sensitivity has evolved as a regulatory mechanism for some of this large family, but not others.
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Affiliation(s)
- Sarah H Ross
- Division of Molecular Physiology, College of Life Sciences, University of Dundee, Dundee, UK
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26
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Puhl AA, Gruninger RJ, Greiner R, Janzen TW, Mosimann SC, Selinger LB. Kinetic and structural analysis of a bacterial protein tyrosine phosphatase-like myo-inositol polyphosphatase. Protein Sci 2007; 16:1368-78. [PMID: 17567745 PMCID: PMC2206706 DOI: 10.1110/ps.062738307] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PhyA from Selenomonas ruminantium (PhyAsr), is a bacterial protein tyrosine phosphatase (PTP)-like inositol polyphosphate phosphatase (IPPase) that is distantly related to known PTPs. PhyAsr has a second substrate binding site referred to as a standby site and the P-loop (HCX5R) has been observed in both open (inactive) and closed (active) conformations. Site-directed mutagenesis and kinetic and structural studies indicate PhyAsr follows a classical PTP mechanism of hydrolysis and has a broad specificity toward polyphosphorylated myo-inositol substrates, including phosphoinositides. Kinetic and molecular docking experiments demonstrate PhyAsr preferentially cleaves the 3-phosphate position of Ins P6 and will produce Ins(2)P via a highly ordered series of sequential dephosphorylations: D-Ins(1,2,4,5,6)P5, Ins(2,4,5,6)P4, D-Ins(2,4,5)P3, and D-Ins(2,4)P2. The data support a distributive enzyme mechanism and suggest the PhyAsr standby site is involved in the recruitment of substrate. Structural studies at physiological pH and high salt concentrations demonstrate the "closed" or active P-loop conformation can be induced in the absence of substrate. These results suggest PhyAsr should be reclassified as a D-3 myo-inositol hexakisphosphate phosphohydrolase and suggest the PhyAsr reaction mechanism is more similar to that of PTPs than previously suspected.
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Affiliation(s)
- Aaron A Puhl
- Department of Biological Sciences, University of Lethbridge, Alberta, Canada
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27
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Grundner C, Perrin D, van Huijsduijnen RH, Swinnen D, Gonzalez J, Gee CL, Wells TN, Alber T. Structural basis for selective inhibition of Mycobacterium tuberculosis protein tyrosine phosphatase PtpB. Structure 2007; 15:499-509. [PMID: 17437721 PMCID: PMC2775457 DOI: 10.1016/j.str.2007.03.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 03/05/2007] [Accepted: 03/07/2007] [Indexed: 01/07/2023]
Abstract
Tyrosine kinases and phosphatases establish the crucial balance of tyrosine phosphorylation in cellular signaling, but creating specific inhibitors of protein Tyr phosphatases (PTPs) remains a challenge. Here, we report the development of a potent, selective inhibitor of Mycobacterium tuberculosis PtpB, a bacterial PTP that is secreted into host cells where it disrupts unidentified signaling pathways. The inhibitor, (oxalylamino-methylene)-thiophene sulfonamide (OMTS), showed an IC(50) of 440 +/- 50 nM and >60-fold specificity for PtpB over six human PTPs. The 2 A resolution crystal structure of PtpB in complex with OMTS revealed a large rearrangement of the enzyme, with some residues shifting >27 A relative to the PtpB:PO(4) complex. Extensive contacts with the catalytic loop provide a potential basis for inhibitor selectivity. Two OMTS molecules bound adjacent to each other, raising the possibility of a second substrate phosphotyrosine binding site in PtpB. The PtpB:OMTS structure provides an unanticipated framework to guide inhibitor improvement.
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Affiliation(s)
- Christoph Grundner
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | | | | | | | | | - Christine L. Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | | | - Tom Alber
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Corresponding author: 510-642-8758 (Voice), 510-643-9290 (FAX),
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28
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Zhang W, Tong Q, Conrad K, Wozney J, Cheung JY, Miller BA. Regulation of TRP channel TRPM2 by the tyrosine phosphatase PTPL1. Am J Physiol Cell Physiol 2007; 292:C1746-58. [PMID: 17251321 DOI: 10.1152/ajpcell.00569.2006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
TRPM2, a member of the transient receptor potential (TRP) superfamily, is a Ca(2+)-permeable channel, which mediates susceptibility to cell death following activation by oxidative stress, TNFalpha, or beta-amyloid peptide. We determined that TRPM2 is rapidly tyrosine phosphorylated after stimulation with H(2)O(2) or TNFalpha. Inhibition of tyrosine phosphorylation with the tyrosine kinase inhibitors genistein or PP2 significantly reduced the increase in [Ca(2+)](i) observed after H(2)O(2) or TNFalpha treatment in TRPM2-expressing cells, suggesting that phosphorylation is important in TRPM2 activation. Utilizing a TransSignal PDZ domain array blot to identify proteins which interact with TRPM2, we identified PTPL1 as a potential binding protein. PTPL1 is a widely expressed tyrosine phosphatase, which has a role in cell survival and tumorigenesis. Immunoprecipitation and glutathione-S-transferase pull-down assays confirmed that TRPM2 and PTPL1 interact. To examine the ability of PTPL1 to modulate phosphorylation or activation of TRPM2, PTPL1 was coexpressed with TRPM2 in human embryonic kidney-293T cells. This resulted in significantly reduced TRPM2 tyrosine phosphorylation, and inhibited the rise in [Ca(2+)](i) and the loss of cell viability, which follow H(2)O(2) or TNFalpha treatment. Consistent with these findings, reduction in endogenous PTPL1 expression with small interfering RNA resulted in increased TRPM2 tyrosine phosphorylation, a significantly greater rise in [Ca(2+)](i) following H(2)O(2) treatment, and enhanced susceptibility to H(2)O(2)-induced cell death. Endogenous TRPM2 and PTPL1 was associated in U937-ecoR cells, confirming the physiological relevance of this interaction. These data demonstrate that tyrosine phosphorylation of TRPM2 is important in its activation and function and that inhibition of TRPM2 tyrosine phosphorylation reduces Ca(2+) influx and protects cell viability. They also suggest that modulation of TRPM2 tyrosine phosphorylation is a mechanism through which PTPL1 may mediate resistance to cell death.
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Affiliation(s)
- Wenyi Zhang
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Milton S. Hershey Medical Center, PO Box 850, Hershey, PA 17033, USA
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29
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Abstract
Following the discovery of insulin, it took the rest of the twentieth century to understand how this hormone regulates intracellular metabolism. What are the main discoveries that led to our current understanding of this process? And how is this new knowledge being exploited in an attempt to develop improved drugs to treat the epidemic of type-2 diabetes?
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Affiliation(s)
- Philip Cohen
- Medical Research Council Protein Phosphorylation Unit, College of Life Sciences, The Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland, UK.
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30
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Wickramasinghe S, Inglis K, Urch J, Müller S, van Aalten D, Fairlamb A. Kinetic, inhibition and structural studies on 3-oxoacyl-ACP reductase from Plasmodium falciparum, a key enzyme in fatty acid biosynthesis. Biochem J 2006; 393:447-57. [PMID: 16225460 PMCID: PMC1360695 DOI: 10.1042/bj20050832] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Revised: 09/26/2005] [Accepted: 10/14/2005] [Indexed: 01/31/2023]
Abstract
Type II fatty acid biosynthesis represents an attractive target for the discovery of new antimalarial drugs. Previous studies have identified malarial ENR (enoyl acyl-carrier-protein reductase, or FabI) as the target for the antiseptic triclosan. In the present paper, we report the biochemical properties and 1.5 A (1 A=0.1 nm) crystal structure of OAR (3-oxoacyl acyl-carrier-protein reductase, or FabG), the second reductive step in fatty acid biosynthesis and its inhibition by hexachlorophene. Under optimal conditions of pH and ionic strength, Plasmodium falciparum OAR displays kinetic properties similar to those of OAR from bacteria or plants. Activity with NADH is <3% of that with NADPH. Fluorescence enhancement studies indicate that NADPH can bind to the free enzyme, consistent with kinetic and product inhibition studies suggesting a steady-state ordered mechanism. The crystal structure reveals a tetramer with a sulphate ion bound in the cofactor-binding site such that the side chains of the catalytic triad of serine, tyrosine and lysine are aligned in an active conformation, as previously observed in the Escherichia coli OAR-NADP+ complex. A cluster of positively charged residues is positioned at the entrance to the active site, consistent with the proposed recognition site for the physiological substrate (3-oxoacyl-acyl-carrier protein) in E. coli OAR. The antibacterial and anthelminthic agent hexachlorophene is a potent inhibitor of OAR (IC50 2.05 microM) displaying non-linear competitive inhibition with respect to NADPH. Hexachlorophene (EC50 6.2 microM) and analogues such as bithionol also have antimalarial activity in vitro, suggesting they might be useful leads for further development.
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Key Words
- acetoacetyl-coa
- fatty acid biosynthesis
- hexachlorophene
- malaria
- nadph
- plasmodium falciparum
- acaccoa, acetoacetyl-coa
- acacnac, n-acetyl-s-acetoacetyl cysteamine
- acp, acyl-carrier protein
- auc, analytical ultracentrifugation
- dtt, dithiothreitol
- enr, enoyl-acp reductase
- fas, fatty acid synthase
- kas iii, β-ketoacyl-acp synthase iii
- maldi–tof, matrix-assisted laser-desorption ionization–time-of-flight
- mcat, malonyl-coa:acp transcylase
- oar, 3-oxoacyl-acp reductase
- r.m.s.d., root mean square deviation
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Affiliation(s)
- Sasala R. Wickramasinghe
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Kirstine A. Inglis
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Jonathan E. Urch
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Sylke Müller
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Daan M. F. van Aalten
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Alan H. Fairlamb
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
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Ivanov VN, Ronai Z, Hei TK. Opposite roles of FAP-1 and dynamin in the regulation of Fas (CD95) translocation to the cell surface and susceptibility to Fas ligand-mediated apoptosis. J Biol Chem 2005; 281:1840-52. [PMID: 16306044 PMCID: PMC4376329 DOI: 10.1074/jbc.m509866200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human melanoma is the most aggressive form of skin cancer and is extremely resistant to radiation and chemotherapy. One of the critical parameters of this resistance is down-regulation of Fas (CD95) cell-surface expression. Using TIG3 normal human fibroblasts and human melanoma cell lines, we investigated transcriptional regulation of FAP-1, a regulator of Fas translocation in the cell. Protein-tyrosine phosphatase FAP-1 (PTPN13, PTP-BAS) interacts with human Fas protein and prevents its export from the cytoplasm to the cell surface. In contrast, dynamin-2 facilitates Fas protein translocation from the Golgi apparatus via the trans-Golgi network to the cell surface. Suppression of dynamin functions by dominant negative dynamin K44A blocks Fas export, whereas the down-regulation of FAP-1 expression by specific RNA interference restores Fas export (a phenomenon that could still be down-regulated in the presence of dominant-negative dynamin). Based on the FAP-1- and dynamin-dependent regulation of Fas translocation, we have created human melanoma lines with different levels of surface expression of Fas. Treatment of these melanoma lines with soluble Fas ligand resulted in programmed cell death that was proportional to the pre-existing levels of surface Fas. Taking into consideration the well known observations that FAP-1 expression is often up-regulated in metastatic tumors, we have established a causal connection between high basal NF-kappaB transcription factor activity (which is a hallmark of many types of metastatic tumors) and NF-kappaB-dependent transcriptional regulation of FAP-1 gene expression that finally restricts Fas protein trafficking, thereby, facilitating the survival of cancer cells.
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Affiliation(s)
- Vladimir N Ivanov
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA.
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Mustelin T, Tautz L, Page R. Structure of the Hematopoietic Tyrosine Phosphatase (HePTP) Catalytic Domain: Structure of a KIM Phosphatase with Phosphate Bound at the Active Site. J Mol Biol 2005; 354:150-63. [PMID: 16226275 DOI: 10.1016/j.jmb.2005.09.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 09/14/2005] [Accepted: 09/16/2005] [Indexed: 10/25/2022]
Abstract
Hematopoietic tyrosine phosphatase (HePTP) is a 38kDa class I non-receptor protein tyrosine phosphatase (PTP) that is strongly expressed in T cells. It is composed of a C-terminal classical PTP domain (residues 44-339) and a short N-terminal extension (residues 1-43) that functions to direct HePTP to its physiological substrates. Moreover, HePTP is a member of a recently identified family of PTPs that has a major role in regulating the activity and translocation of the MAP kinases Erk and p38. HePTP binds Erk and p38 via a short, highly conserved motif in its N terminus, termed the kinase interaction motif (KIM). Association of HePTP with Erk via the KIM results in an unusual, reciprocal interaction between the two proteins. First, Erk phosphorylates HePTP at residues Thr45 and Ser72. Second, HePTP dephosphorylates Erk at PTyr185. In order to gain further insight into the interaction of HePTP with Erk, we determined the structure of the PTP catalytic domain of HePTP, residues 44-339. The HePTP catalytic phosphatase domain displays the classical PTP1B fold and superimposes well with PTP-SL, the first KIM-containing phosphatase solved to high resolution. In contrast to the PTP-SL structure, however, HePTP crystallized with a well-ordered phosphate ion bound at the active site. This resulted in the closure of the catalytically important WPD loop, and thus, HePTP represents the first KIM-containing phosphatase solved in the closed conformation. Finally, using this structure of the HePTP catalytic domain, we show that both the phosphorylation of HePTP at Thr45 and Ser72 by Erk2 and the dephosphorylation of Erk2 at Tyr185 by HePTP require significant conformational changes in both proteins.
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Affiliation(s)
- Tomas Mustelin
- Program of Inflammation, The Burnham Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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