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Welsh CL, Madan LK. Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. J Chem Inf Model 2024; 64:1331-1346. [PMID: 38346324 DOI: 10.1021/acs.jcim.3c01615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Dynamics-driven allostery provides important insights into the working mechanics of proteins, especially enzymes. In this study, we employ this paradigm to answer a basic question: in enzyme superfamilies, where the catalytic mechanism, active sites, and protein fold are conserved, what accounts for the difference in the catalytic prowess of the individual members? We show that when subtle changes in sequence do not translate to changes in structure, they do translate to changes in dynamics. We use sequentially diverse PTP1B, TbPTP1, and YopH as representatives of the conserved protein tyrosine phosphatase (PTP) superfamily. Using amino acid network analysis of group behavior (community analysis) and influential node dominance on networks (eigenvector centrality), we explain the dynamic basis of the catalytic variations seen between the three proteins. Importantly, we explain how a dynamics-based blueprint makes PTP1B amenable to allosteric control and how the same is abstracted in TbPTP1 and YopH.
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Affiliation(s)
- Colin L Welsh
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, United States
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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2
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Welsh CL, Madan LK. Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. bioRxiv 2023:2023.07.23.550226. [PMID: 37547015 PMCID: PMC10402003 DOI: 10.1101/2023.07.23.550226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Dynamics-driven allostery provides important insights into the working mechanics of proteins, especially enzymes. In this study we employ this paradigm to answer a basic question: in enzyme superfamilies where the catalytic mechanism, active sites and protein fold are conserved, what accounts for the difference in the catalytic prowess of the individual members? We show that when subtle changes in sequence do not translate to changes in structure, they do translate to changes in dynamics. We use sequentially diverse PTP1B, TbPTP1, and YopH as the representatives of the conserved Protein Tyrosine Phosphatase (PTP) superfamily. Using amino acid network analysis of group behavior (community analysis) and influential node dominance on networks (eigenvector centrality), we explain the dynamic basis of catalytic variations seen between the three proteins. Importantly, we explain how a dynamics-based blueprint makes PTP1B amenable to allosteric control and how the same is abstracted in TbPTP1 and YopH.
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Abstract
Protein tyrosine phosphatases (PTPs) play an important role in cellular signaling and have been implicated in human cancers, diabetes, and obesity. Despite shared catalytic mechanisms and transition states for the chemical steps of catalysis, catalytic rates within the PTP family vary over several orders of magnitude. These rate differences have been implied to arise from differing conformational dynamics of the closure of a protein loop, the WPD-loop, which carries a catalytically critical residue. The present work reports computational studies of the human protein tyrosine phosphatase 1B (PTP1B) and YopH from Yersinia pestis, for which NMR has demonstrated a link between their respective rates of WPD-loop motion and catalysis rates, which differ by an order of magnitude. We have performed detailed structural analysis, both conventional and enhanced sampling simulations of their loop dynamics, as well as empirical valence bond simulations of the chemical step of catalysis. These analyses revealed the key residues and structural features responsible for these differences, as well as the residues and pathways that facilitate allosteric communication in these enzymes. Curiously, our wild-type YopH simulations also identify a catalytically incompetent hyper-open conformation of its WPD-loop, sampled as a rare event, previously only experimentally observed in YopH-based chimeras. The effect of differences within the WPD-loop and its neighboring loops on the modulation of loop dynamics, as revealed in this work, may provide a facile means for the family of PTP enzymes to respond to environmental changes and regulate their catalytic activities.
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Affiliation(s)
- Rory M. Crean
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
| | - Michal Biler
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
| | - Marc W. van der Kamp
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, University
Walk, Bristol BS8 1TD, United Kingdom
| | - Alvan C. Hengge
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322-0300, United States
| | - Shina C. L. Kamerlin
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
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Zhang X, Yu Y, Bai B, Wang T, Zhao J, Zhang N, Zhao Y, Wang X, Wang B. PTPN22 interacts with EB1 to regulate T-cell receptor signaling. FASEB J 2020; 34:8959-8974. [PMID: 32469452 DOI: 10.1096/fj.201902811rr] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/14/2020] [Accepted: 03/18/2020] [Indexed: 12/21/2022]
Abstract
The PTPN22 gene encoding the Lyp/Pep protein tyrosine phosphatase is a negative regulator of T-cell receptor (TCR) signaling. Recent studies have shown that phosphorylation of end-binding protein 1 (EB1) is associated with the TCR activation. In this study, using 2-hybrid and mass spectrometry analyses, we identified EB1 as a protein associated with PTPN22. Furthermore, we discovered that EB1 specifically bound to the P1 domain of PTPN22 by competing with CSK, and the variant PTPN22-R620W does not affect the association with EB1, which is instrumental with respect to the regulation of TCR signaling. In addition, PTPN22 dephosphorylates EB1 at tyrosine-247 (Y247), which decreases the expression of the T-cell activation markers CD25 and CD69 and the phosphorylation levels of the TCR molecules ZAP-70, LAT, and Erk, leading to the eventual downregulation of the transcription factor NFAT and reduced the levels of secreted IL-2. The findings of this study provide new insights into the TCR signaling and the T-cell immune response, which are important for clarifying the mechanism of PTPN22-related autoimmune diseases.
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Affiliation(s)
- Xiaonan Zhang
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Yang Yu
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Bin Bai
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Tao Wang
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Jiahui Zhao
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Na Zhang
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Yanjiao Zhao
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Xipeng Wang
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Bing Wang
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
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5
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Yang D, Xiao P, Li Q, Fu X, Pan C, Lu D, Wen S, Xia W, He D, Li H, Fang H, Shen Y, Xu Z, Lin A, Wang C, Yu X, Wu J, Sun J. Allosteric modulation of the catalytic VYD loop in Slingshot by its N-terminal domain underlies both Slingshot auto-inhibition and activation. J Biol Chem 2018; 293:16226-16241. [PMID: 30154244 DOI: 10.1074/jbc.ra118.004175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/21/2018] [Indexed: 12/22/2022] Open
Abstract
Slingshots are phosphatases that modulate cytoskeleton dynamics, and their activities are tightly regulated in different physiological contexts. Recently, abnormally elevated Slingshot activity has been implicated in many human diseases, such as cancer, Alzheimer's disease, and vascular diseases. Therefore, Slingshot-specific inhibitors have therapeutic potential. However, an enzymological understanding of the catalytic mechanism of Slingshots and of their activation by actin is lacking. Here, we report that the N-terminal region of human Slingshot2 auto-inhibits its phosphatase activity in a noncompetitive manner. pH-dependent phosphatase assays and leaving-group dependence studies suggested that the N-terminal domain of Slingshot2 regulates the stability of the leaving group of the product during catalysis by modulating the general acid Asp361 in the catalytic VYD loop. F-actin binding relieved this auto-inhibition and restored the function of the general acid. Limited tryptic digestion and biophysical studies identified large conformational changes in Slingshot2 after the F-actin binding. The dissociation of N-terminal structural elements, including Leu63, and the exposure of the loop between α-helix-2 and β-sheet-3 of the phosphatase domain served as the structural basis for Slingshot activation via F-actin binding in vitro and via neuregulin stimulation in cells. Moreover, we designed a FlAsH-BRET-based Slingshot2 biosensor whose readout was highly correlated with the in vivo phosphatase activities of Slingshot2. Our results reveal the auto-inhibitory mechanism and allosteric activation mechanisms of a human Slingshot phosphatase. They also contribute to the design of new strategies to study Slingshot regulation in various cellular contexts and to screen for new activators/inhibitors of Slingshot activity.
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Affiliation(s)
- Duxiao Yang
- From the Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, and
| | - Peng Xiao
- From the Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, and.,the School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Qing Li
- the Department of Physiology, Shandong University School of Medicine, Jinan, Shandong 250012, China
| | - Xiaolei Fu
- From the Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, and
| | - Chang Pan
- From the Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, and
| | - Di Lu
- From the Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, and
| | - Shishuai Wen
- the School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Wanying Xia
- From the Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, and
| | - Dongfang He
- From the Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, and
| | - Hui Li
- the Department of Physiology, Shandong University School of Medicine, Jinan, Shandong 250012, China
| | - Hao Fang
- the School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Yuemao Shen
- the School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Zhigang Xu
- the School of Life Science, Shandong University, Jinan, Shandong 250003, China
| | - Amy Lin
- the School of Medicine, Duke University, Durham, North Carolina 27705
| | - Chuan Wang
- the Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Xiao Yu
- the Department of Physiology, Shandong University School of Medicine, Jinan, Shandong 250012, China
| | - Jiawei Wu
- the MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jinpeng Sun
- From the Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, and .,the Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing 100191, China, and.,the Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, Beijing 100191, China
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6
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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] [What about the content of this article? (0)] [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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7
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Tahtah Y, Wubshet SG, Kongstad KT, Heskes AM, Pateraki I, Møller BL, Jäger AK, Staerk D. High-resolution PTP1B inhibition profiling combined with high-performance liquid chromatography-high-resolution mass spectrometry-solid-phase extraction-nuclear magnetic resonance spectroscopy: Proof-of-concept and antidiabetic constituents in crude extract of Eremophila lucida. Fitoterapia 2016; 110:52-8. [PMID: 26882973 DOI: 10.1016/j.fitote.2016.02.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 01/02/2023]
Abstract
Type 2 diabetes (T2D) constituted 90% of the global 387 million diabetes cases in 2014. The enzyme protein-tyrosine phosphatase 1B (PTP1B) has been recognized as a therapeutic target for treatment of T2D and its adverse complications. With the aim of accelerating the investigation of complex natural sources, such as crude plant extracts, for potential PTP1B inhibitors, we have developed a bio-analytical platform combining high-resolution PTP1B inhibition profiling and high-performance liquid chromatography-high-resolution mass spectrometry-solid-phase extraction-nuclear magnetic resonance spectroscopy, i.e., HR-bioassay/HPLC-HRMS-SPE-NMR. Human recombinant PTP1B enzyme was used for the microplate-based PTP1B inhibition assay, which was optimized for pH and substrate concentration to be compatible with rate measurements within the 10 min incubation time. Subsequently, analytical-scale HPLC-based microfractionation followed by colorimetric microplate-based PTP1B bioassaying enabled construction of a high-resolution inhibition profile corresponding to the HPLC profile. The high-resolution PTP1B inhibition profiling was validated using an artificial mixture of known PTP1B inhibitors and non-inhibiting compounds as negative controls. Finally, a proof-of-concept study with a real sample was performed using crude ethyl acetate extract of the phytochemically hitherto unexplored plant Eremophila lucida. This led to the identification of the first viscidane type diterpene, i.e., 5-hydroxyviscida-3,14-dien-20-oic acid (9) as PTP1B inhibitor with an IC50 value of 42.0 ± 5.9 μM. In addition, a series of flavonoids, i.e., luteolin (1), dinatin (3a), tricin (3b), 3,6-dimethoxyapigenin (4), jaceidin (5), and cirsimaritin (6) as well as a cembrene diterpene, (3Z, 7E, 11Z)-15-hydroxycembra-3,7,11-trien-19-oic acid (8), were also identified for the first time from E. lucida.
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8
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McLauchlan CC, Peters BJ, Willsky GR, Crans DC. Vanadium–phosphatase complexes: Phosphatase inhibitors favor the trigonal bipyramidal transition state geometries. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2014.12.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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9
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Wagner S, Schütz A, Rademann J. Light-switched inhibitors of protein tyrosine phosphatase PTP1B based on phosphonocarbonyl phenylalanine as photoactive phosphotyrosine mimetic. Bioorg Med Chem 2015; 23:2839-47. [PMID: 25907367 DOI: 10.1016/j.bmc.2015.03.074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 11/24/2022]
Abstract
Phosphopeptide mimetics containing the 4-phosphonocarbonyl phenylalanine (pcF) as a photo-active phosphotyrosine isoster are developed as potent, light-switchable inhibitors of the protein tyrosine phosphatase PTP1B. The photo-active inhibitors 6-10 are derived from phosphopeptide substrates and are prepared from the suitably protected pcF building block 12 by Fmoc-based solid phase peptide synthesis. All pcF-containing peptides are moderate inhibitors of PTP1B with KI values between 10 and 50μM. Irradiation of the inhibitors at 365nm in the presence of the protein PTP1B amplify the inhibitory activity of pcF-peptides up to 120-fold, switching the KI values of the best inhibitors to the sub-micromolar range. Photo-activation of the inhibitors results in the formation of triplet intermediates of the benzoylphosphonate moiety, which deactivate PTP1B following an oxidative radical mechanism. Deactivation of PTP1B proceeds without covalent crosslinking of the protein target with the photo-switched inhibitors and can be reverted by subsequent addition of reducing agent dithiothreitol (DTT).
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Affiliation(s)
- Stefan Wagner
- Freie Universität Berlin, Institute of Pharmacy, Medicinal Chemistry, Königin-Luise-Str. 2+4, 14195 Berlin, Germany
| | - Anja Schütz
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Jörg Rademann
- Freie Universität Berlin, Institute of Pharmacy, Medicinal Chemistry, Königin-Luise-Str. 2+4, 14195 Berlin, Germany.
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10
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Pan C, Tang JY, Xu YF, Xiao P, Liu HD, Wang HA, Wang WB, Meng FG, Yu X, Sun JP. The catalytic role of the M2 metal ion in PP2Cα. Sci Rep 2015; 5:8560. [PMID: 25708299 PMCID: PMC5390078 DOI: 10.1038/srep08560] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/26/2015] [Indexed: 01/16/2023] Open
Abstract
PP2C family phosphatases (the type 2C family of protein phosphatases; or metal-dependent phosphatase, PPM) constitute an important class of signaling enzymes that regulate many fundamental life activities. All PP2C family members have a conserved binuclear metal ion active center that is essential for their catalysis. However, the catalytic role of each metal ion during catalysis remains elusive. In this study, we discovered that mutations in the structurally buried D38 residue of PP2Cα (PPM1A) redefined the water-mediated hydrogen network in the active site and selectively disrupted M2 metal ion binding. Using the D38A and D38K mutations of PP2Cα as specific tools in combination with enzymology analysis, our results demonstrated that the M2 metal ion determines the rate-limiting step of substrate hydrolysis, participates in dianion substrate binding and stabilizes the leaving group after P-O bond cleavage. The newly characterized catalytic role of the M2 metal ion in this family not only provides insight into how the binuclear metal centers of the PP2C phosphatases are organized for efficient catalysis but also helps increase our understanding of the function and substrate specificity of PP2C family members.
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Affiliation(s)
- Chang Pan
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Qilu Hospital of Shandong University, Jinan, China
| | - Jun-yi Tang
- 1] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China [2] Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Yun-fei Xu
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Qilu Hospital of Shandong University, Jinan, China
| | - Peng Xiao
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Hong-da Liu
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Qilu Hospital of Shandong University, Jinan, China [3] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Hao-an Wang
- Department of Human Biology, University of Toronto, Toronto, Ontario, Canada
| | - Wen-bo Wang
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Qilu Hospital of Shandong University, Jinan, China [3] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Fan-guo Meng
- Yangtze Delta Region Institute of Tsinghua University, Zhejiang, China
| | - Xiao Yu
- 1] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China [2] Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Jin-peng Sun
- 1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China [3] Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
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11
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Xiao P, Wang X, Wang HM, Fu XL, Cui FA, Yu X, Wen SS, Bi WX, Sun JP. The second-sphere residue T263 is important for the function and catalytic activity of PTP1B via interaction with the WPD-loop. Int J Biochem Cell Biol 2014; 57:84-95. [PMID: 25450460 DOI: 10.1016/j.biocel.2014.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/21/2014] [Accepted: 10/04/2014] [Indexed: 10/24/2022]
Abstract
Protein tyrosine phosphatases have diverse substrate specificities and intrinsic activities that lay the foundations for the fine-tuning of a phosphorylation network to precisely regulate cellular signal transduction. All classical PTPs share common catalytic mechanisms, and the important catalytic residues in the first sphere of their active sites have been well characterized. However, little attention has been paid to the second-sphere residues that are potentially important in defining the intrinsic activity and substrate specificity of PTPs. Here, we find that a conserved second-sphere residue, Thr263, located in the surface Q-loop is important for both the function and activity of PTPs. Using PTP1B as a study model, we found that mutations of Thr263 impaired the negative regulation role of PTP1B in insulin signaling. A detailed mechanistic study utilizing steady-state kinetics, Brønsted analysis and pH dependence in the presence of pNPP or phosphopeptide substrates revealed that Thr263 is required for the stabilization of the leaving group during catalysis. Further crystallographic studies and structural comparison revealed that Thr263 regulates the general acid function through modulation of the WPD-loop by the T263:F182/Y/H interaction pair, which is conserved in 26 out of 32 classical PTPs. In addition, the hydrophobic interaction between Thr263 and Arg1159 of the insulin receptor contributes to the substrate specificity of PTP1B. Taken together, our findings demonstrate the general role of the second-sphere residue Thr263 in PTP catalysis. Our findings suggest that the second sphere residues of PTP active site may play important roles in PTP-mediated function in both normal and diseased states.
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Affiliation(s)
- Peng Xiao
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China; Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Xiao Wang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China; Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Hong-Mei Wang
- Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China; Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Xiao-Lei Fu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China; Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China; Department of Public Health, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Fu-ai Cui
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Xiao Yu
- Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China; Department of Public Health, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Shi-shuai Wen
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China; Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Wen-Xiang Bi
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China.
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China; Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China; Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China.
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12
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Li S, Zhang J, Lu S, Huang W, Geng L, Shen Q, Zhang J. The mechanism of allosteric inhibition of protein tyrosine phosphatase 1B. PLoS One 2014; 9:e97668. [PMID: 24831294 PMCID: PMC4022711 DOI: 10.1371/journal.pone.0097668] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/09/2014] [Indexed: 11/24/2022] Open
Abstract
As the prototypical member of the PTP family, protein tyrosine phosphatase 1B (PTP1B) is an attractive target for therapeutic interventions in type 2 diabetes. The extremely conserved catalytic site of PTP1B renders the design of selective PTP1B inhibitors intractable. Although discovered allosteric inhibitors containing a benzofuran sulfonamide scaffold offer fascinating opportunities to overcome selectivity issues, the allosteric inhibitory mechanism of PTP1B has remained elusive. Here, molecular dynamics (MD) simulations, coupled with a dynamic weighted community analysis, were performed to unveil the potential allosteric signal propagation pathway from the allosteric site to the catalytic site in PTP1B. This result revealed that the allosteric inhibitor compound-3 induces a conformational rearrangement in helix α7, disrupting the triangular interaction among helix α7, helix α3, and loop11. Helix α7 then produces a force, pulling helix α3 outward, and promotes Ser190 to interact with Tyr176. As a result, the deviation of Tyr176 abrogates the hydrophobic interactions with Trp179 and leads to the downward movement of the WPD loop, which forms an H-bond between Asp181 and Glu115. The formation of this H-bond constrains the WPD loop to its open conformation and thus inactivates PTP1B. The discovery of this allosteric mechanism provides an overall view of the regulation of PTP1B, which is an important insight for the design of potent allosteric PTP1B inhibitors.
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Affiliation(s)
- Shuai Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Jingmiao Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Wenkang Huang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Lv Geng
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Qiancheng Shen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China; Medicinal Bioinformatics Center, Shanghai JiaoTong University, School of Medicine, Shanghai, China
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Abstract
Protein tyrosine phosphorylation is a key regulatory mechanism in eukaryotic cell physiology. Aberrant expression or function of protein tyrosine kinases and protein tyrosine phosphatases can lead to serious human diseases, including cancer, diabetes, as well as cardiovascular, infectious, autoimmune, and neuropsychiatric disorders. Here, we give an overview of the protein tyrosine phosphatase superfamily with its over 100 members in humans. We review their structure, function, and implications in human diseases, and discuss their potential as novel drug targets, as well as current challenges and possible solutions to developing therapeutics based on these enzymes.
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Affiliation(s)
- Lutz Tautz
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
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14
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Brandão TAS, Johnson SJ, Hengge AC. The molecular details of WPD-loop movement differ in the protein-tyrosine phosphatases YopH and PTP1B. Arch Biochem Biophys 2012; 525:53-9. [PMID: 22698963 PMCID: PMC3422214 DOI: 10.1016/j.abb.2012.06.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/03/2012] [Accepted: 06/04/2012] [Indexed: 11/21/2022]
Abstract
The movement of a conserved protein loop (the WPD-loop) is important in catalysis by protein tyrosine phosphatases (PTPs). Using kinetics, isotope effects, and X-ray crystallography, the different effects arising from mutation of the conserved tryptophan in the WPD-loop were compared in two PTPs, the human PTP1B, and the bacterial YopH from Yersinia. Mutation of the conserved tryptophan in the WPD-loop to phenylalanine has a negligible effect on k(cat) in PTP1B and full loop movement is maintained. In contrast, the corresponding mutation in YopH reduces k(cat) by two orders of magnitude and the WPD loop locks in an intermediate position, disabling general acid catalysis. During loop movement the indole moiety of the WPD-loop tryptophan moves in opposite directions in the two enzymes. Comparisons of mammalian and bacterial PTPs reveal differences in the residues forming the hydrophobic pocket surrounding the conserved tryptophan. Thus, although WPD-loop movement is a conserved feature in PTPs, differences exist in the molecular details, and in the tolerance to mutation, in PTP1B compared to YopH. Despite high structural similarity of the active sites in both WPD-loop open and closed conformations, differences are identified in the molecular details associated with loop movement in PTPs from different organisms.
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Affiliation(s)
- Tiago A. S. Brandão
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300
- Departamento de Química, ICEX, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Sean J. Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300
| | - Alvan C. Hengge
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300
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15
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Liu J, Chen M, Li R, Yang F, Shi X, Zhu L, Wang HM, Yao W, Liu Q, Meng FG, Sun JP, Pang Q, Yu X. Biochemical and functional studies of lymphoid-specific tyrosine phosphatase (Lyp) variants S201F and R266W. PLoS One 2012; 7:e43631. [PMID: 22952725 PMCID: PMC3428364 DOI: 10.1371/journal.pone.0043631] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Accepted: 07/23/2012] [Indexed: 11/21/2022] Open
Abstract
The Lymphoid specific tyrosine phosphatase (Lyp) has elicited tremendous research interest due to the high risk of its missense mutation R620W in a wide spectrum of autoimmune diseases. While initially characterized as a gain-of-function mutant, R620W was thought to lead to autoimmune diseases through loss-of-function in T cell signaling by a recent study. Here we investigate the biochemical characters and T cell signaling functions of two uncharacterized Lyp variants S201F and R266W, together with a previously characterized Lyp variant R263Q, which had reduced risk in several autoimmune diseases, including systemic lupus erythematosus (SLE), ulcerative colitis (UC) and rheumatoid arthritis (RA). Our kinetic and functional studies of R263Q polymorphism basically reproduced previous findings that it was a loss-of-function mutant. The other variant S201F reduced Lyp phosphatase activity moderately and decreased Lyp function in T cell slightly, while R266W severely impaired phosphatase activity and was a loss-of-function variant in T cell signaling. A combined kinetic and structure analysis suggests that the R266W variant may decrease its phosphatase activity through perturbing either the Q-loop or the WPD loop of Lyp. As both R266W and R263Q significantly change their phosphatase activity and T cell functions, future work could be considered to evaluate these mutants in a broader spectrum of autoimmune diseases.
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Affiliation(s)
- Jing Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Ming Chen
- The 309 Hospital of PLA, Beijing, China
| | - Rong Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Fan Yang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Xuanren Shi
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Lichao Zhu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Hong-Mei Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Wei Yao
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Qiji Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Fan-Guo Meng
- Yangtze Delta Region Institute of Tsinghua University, Zhejiang, China
| | - Jin-Peng Sun
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
- Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Qi Pang
- Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
- * E-mail: (XY); (QP)
| | - Xiao Yu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
- * E-mail: (XY); (QP)
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16
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Sobhia ME, Paul S, Shinde R, Potluri M, Gundam V, Kaur A, Haokip T. Protein tyrosine phosphatase inhibitors: a patent review (2002 – 2011). Expert Opin Ther Pat 2012; 22:125-53. [DOI: 10.1517/13543776.2012.661414] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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17
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Brandão TAS, Hengge AC, Johnson SJ. Insights into the reaction of protein-tyrosine phosphatase 1B: crystal structures for transition state analogs of both catalytic steps. J Biol Chem 2010; 285:15874-83. [PMID: 20236928 PMCID: PMC2871455 DOI: 10.1074/jbc.m109.066951] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 03/03/2010] [Indexed: 11/06/2022] Open
Abstract
Catalysis by protein-tyrosine phosphatase 1B (PTP1B) occurs through a two-step mechanism involving a phosphocysteine intermediate. We have solved crystal structures for the transition state analogs for both steps. Together with previously reported crystal structures of apo-PTP1B, the Michaelis complex of an inactive mutant, the phosphoenzyme intermediate, and the product complex, a full picture of all catalytic steps can now be depicted. The transition state analog for the first catalytic step comprises a ternary complex between the catalytic cysteine of PTP1B, vanadate, and the peptide DADEYL, a fragment of a physiological substrate. The equatorial vanadate oxygen atoms bind to the P-loop, and the apical positions are occupied by the peptide tyrosine oxygen and by the PTP1B cysteine sulfur atom. The vanadate assumes a trigonal bipyramidal geometry in both transition state analog structures, with very similar apical O-O distances, denoting similar transition states for both phosphoryl transfer steps. Detailed interactions between the flanking peptide and the enzyme are discussed.
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Affiliation(s)
- Tiago A. S. Brandão
- From the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Alvan C. Hengge
- From the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Sean J. Johnson
- From the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
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18
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Kumar R, Shinde RN, Ajay D, Sobhia ME. Probing Interaction Requirements in PTP1B Inhibitors: A Comparative Molecular Dynamics Study. J Chem Inf Model 2010; 50:1147-58. [DOI: 10.1021/ci900484g] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rajendra Kumar
- Centre for Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab 160062, India
| | - Ranajit Nivrutti Shinde
- Centre for Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab 160062, India
| | - Dara Ajay
- Centre for Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab 160062, India
| | - M. Elizabeth Sobhia
- Centre for Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab 160062, India
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19
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Brandão TAS, Robinson H, Johnson SJ, Hengge AC. Impaired acid catalysis by mutation of a protein loop hinge residue in a YopH mutant revealed by crystal structures. J Am Chem Soc 2009; 131:778-86. [PMID: 19140798 PMCID: PMC2739089 DOI: 10.1021/ja807418b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Catalysis by the Yersinia protein-tyrosine phosphatase YopH is significantly impaired by the mutation of the conserved Trp354 residue to Phe. Though not a catalytic residue, this Trp is a hinge residue in a conserved flexible loop (the WPD-loop) that must close during catalysis. To learn why this seemingly conservative mutation reduces catalysis by 2 orders of magnitude, we have solved high-resolution crystal structures for the W354F YopH in the absence and in the presence of tungstate and vanadate. Oxyanion binding to the P-loop in W354F is analogous to that observed in the native enzyme. However, the WPD-loop in the presence of oxyanions assumes a half-closed conformation, in contrast to the fully closed state observed in structures of the native enzyme. This observation provides an explanation for the impaired general acid catalysis observed in kinetic experiments with Trp mutants. A 1.4 A structure of the W354F mutant obtained in the presence of vanadate reveals an unusual divanadate species with a cyclic [VO](2) core, which has precedent in small molecules but has not been previously reported in a protein crystal structure.
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Affiliation(s)
- Tiago A. S. Brandão
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Howard Robinson
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973-5000
| | - Sean J. Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Alvan C. Hengge
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
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20
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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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21
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Agarwal R, Burley SK, Swaminathan S. Structure of Human Dual Specificity Protein Phosphatase 23, VHZ, Enzyme-Substrate/Product Complex. J Biol Chem 2008; 283:8946-53. [DOI: 10.1074/jbc.m708945200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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22
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Affiliation(s)
- Xin-Yu Zhang
- Department of Chemistry, Amherst College, Amherst, Massachusetts 01002
| | - Anthony C. Bishop
- Department of Chemistry, Amherst College, Amherst, Massachusetts 01002
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23
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Bishop AC, Zhang XY, Lone AM. Generation of inhibitor-sensitive protein tyrosine phosphatases via active-site mutations. Methods 2007; 42:278-88. [PMID: 17532515 PMCID: PMC1950444 DOI: 10.1016/j.ymeth.2007.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 02/14/2007] [Indexed: 01/23/2023] Open
Abstract
Protein tyrosine phosphatases (PTPs) catalyze the dephosphorylation of phosphotyrosine, a central control element in mammalian signal transduction. Small-molecule inhibitors that are specific for each cellular PTP would be valuable tools in dissecting phosphorylation networks and for validating PTPs as therapeutic targets. However, the common architecture of PTP active sites impedes the discovery of selective PTP inhibitors. Our laboratory has recently used enzyme/inhibitor-interface engineering to generate selective PTP inhibitors. The crux of the strategy resides in the design of "inhibitor-sensitized" PTPs through protein engineering of a novel binding pocket in the target PTP. "Allele-specific" inhibitors that selectively target the sensitized PTP can be synthesized by modifying broad-specificity inhibitors with bulky chemical groups that are incompatible with wild-type PTP active sites; alternatively, specific inhibitors that serendipitously recognize the sensitized PTP's non-natural pocket may be discovered from panels of "non-rationally" designed compounds. In this review, we describe the current state of the PTP-sensitization strategy, with emphases on the methodology of identifying PTP-sensitizing mutations and synthesizing the compounds that have been found to target PTPs in an allele-specific manner. Moreover, we discuss the scope of PTP sensitization in regard to the potential application of the approach across the family of classical PTPs.
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Affiliation(s)
- Anthony C Bishop
- Department of Chemistry, Amherst College, Amherst, MA 01002, USA.
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24
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Bishop AC, Blair ER. A gatekeeper residue for inhibitor sensitization of protein tyrosine phosphatases. Bioorg Med Chem Lett 2006; 16:4002-6. [PMID: 16716588 DOI: 10.1016/j.bmcl.2006.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Revised: 05/02/2006] [Accepted: 05/03/2006] [Indexed: 11/23/2022]
Abstract
Allele-specific enzyme inhibitors are powerful tools in chemical biology. However, few general approaches for the discovery of such inhibitors have been described. Herein is reported a method for the sensitization of protein tyrosine phosphatases (PTPs) to small-molecule inhibition. It is shown that mutation of an active-site isoleucine to alanine (I219A) sensitizes PTP1B to inhibition by a class of thiophene-based inhibitors. This sensitization strategy succeeds for both 'orthogonal' inhibitors, designed to be incompatible with wild-type PTP active sites, and previously optimized wild-type PTP inhibitors. The finding that the I219A mutation sensitizes phosphatase domains to a variety of compounds suggests that isoleucine 219 may act as a 'gatekeeper' residue that can be widely exploited for the chemical-genetic analysis of PTP function.
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Affiliation(s)
- Anthony C Bishop
- Department of Chemistry, Amherst College, Amherst, MA 01002, USA.
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Hernández-Hernández A, Garabatos MN, Rodríguez MC, Vidal ML, López-Revuelta A, Sánchez-Gallego JI, Llanillo M, Sánchez-Yagüe J. Structural characteristics of a lipid peroxidation product, trans-2-nonenal, that favour inhibition of membrane-associated phosphotyrosine phosphatase activity. Biochim Biophys Acta Gen Subj 2005; 1726:317-25. [PMID: 16269214 DOI: 10.1016/j.bbagen.2005.09.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 09/28/2005] [Accepted: 09/30/2005] [Indexed: 10/25/2022]
Abstract
Protein-tyrosine phosphatases (PTPs) are very susceptible to oxidation by reactive oxygen species (ROS), which induce the oxidation of catalytic cysteines, thereby inactivating these PTPs. PTPs are also inactivated by treatment with different aldehydes (such as trans-2-nonenal), produced after tissue damage by ROS. However, the molecular mechanisms behind such aldehyde-due inactivation remain unknown. Using commercially available compounds, we examined the structural characteristics of trans-2-nonenal that allow the inhibition of platelet membrane-associated PTP activity, as well as how these compounds affect the dynamics of SH-, CO- and NH2- protein groups on the membranes. PTP was effectively inhibited by physiological amounts of trans-2-nonenal (1-10 microM). Incubation with trans-2-nonene (10 microM) also decreased PTP activity, although to a lower extent. Treatment with nonyl aldehyde almost eliminated PTP inhibition. Decreases in protein thiols were visible after trans-2-nonenal and trans-2-nonene treatments. Both the latter compounds also increased protein carbonyls (although trans-2-nonenal was more effective) and decreased protein amino groups to an equal extent. Collectively, our data indicate that alpha,beta unsaturation (and not a double bond in another position) is the most important structural determinant for PTP inhibition, the alkenal with 9-carbon atoms being the most effective in eliciting such inhibition. The data allow us to predict the modification of sulfhydryls and/or the formation of addition products with lysyl or histidyl residues, and hence the kind of specific antibodies that it would be necessary to generate in order to test such modifications directly.
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Affiliation(s)
- Angel Hernández-Hernández
- Department of Biochemistry and Molecular Biology, University of Salamanca, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
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26
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Blair ER, Hoffman HE, Bishop AC. Engineering non-natural inhibitor sensitivity in protein tyrosine phosphatase H1. Bioorg Med Chem 2005; 14:464-71. [PMID: 16182535 DOI: 10.1016/j.bmc.2005.08.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 08/11/2005] [Accepted: 08/11/2005] [Indexed: 01/10/2023]
Abstract
Protein tyrosine phosphatase H1, a member of the ubiquitous protein tyrosine phosphatase (PTP) superfamily of enzymes, is an important signaling molecule, mutant forms of which have been found in human colorectal cancers. Selective PTPH1 inhibitors would be valuable tools for investigating PTPH1's roles in cellular regulation. However, no PTPH1-specific inhibitors are known. To identify target-selective inhibitors of human PTPH1, we have redesigned a PTPH1/inhibitor interface. Structure-based protein design was used to identify two amino-acid residues, isoleucine 846 and methionine 883, that control PTPH1's sensitivity to oxalylaminoindole PTP inhibitors. Mutation of residues 846 and 883 to alanine and glycine, respectively, conferred novel inhibitor sensitivity onto PTPH1. From a small panel of putative inhibitors, compounds that potently and selectively target the inhibitor-sensitized PTPH1 mutants were identified.
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27
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Abstract
The extracellular signal-regulated protein kinase 2 (ERK2) plays a central role in cellular proliferation and differentiation. Full activation of ERK2 requires dual phosphorylation of Thr183 and Tyr185 in the activation loop. Tyr185 dephosphorylation by the hematopoietic protein-tyrosine phosphatase (HePTP) represents an important mechanism for down-regulating ERK2 activity. The bisphosphorylated ERK2 is a highly efficient substrate for HePTP with a kcat/Km of 2.6 x 10(6) m(-1) s(-1). In contrast, the kcat/Km values for the HePTP-catalyzed hydrolysis of Tyr(P) peptides are 3 orders of magnitude lower. To gain insight into the molecular basis for HePTP substrate specificity, we analyzed the effects of altering structural features unique to HePTP on the HePTP-catalyzed hydrolysis of p-nitrophenyl phosphate, Tyr(P) peptides, and its physiological substrate ERK2. Our results suggest that substrate specificity is conferred upon HePTP by both negative and positive selections. To avoid nonspecific tyrosine dephosphorylation, HePTP employs Thr106 in the substrate recognition loop as a key negative determinant to restrain its protein-tyrosine phosphatase activity. The extremely high efficiency and fidelity of ERK2 dephosphorylation by HePTP is achieved by a bipartite protein-protein interaction mechanism, in which docking interactions between the kinase interaction motif in HePTP and the common docking site in ERK2 promote the HePTP-catalyzed ERK2 dephosphorylation (approximately 20-fold increase in kcat/Km) by increasing the local substrate concentration, and second site interactions between the HePTP catalytic site and the ERK2 substrate-binding region enhance catalysis (approximately 20-fold increase in kcat/Km) by organizing the catalytic residues with respect to Tyr(P)185 for optimal phosphoryl transfer.
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Affiliation(s)
- Zhonghui Huang
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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