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Ren L, Shen D, Liu C, Ding Y. Protein Tyrosine and Serine/Threonine Phosphorylation in Oral Bacterial Dysbiosis and Bacteria-Host Interaction. Front Cell Infect Microbiol 2022; 11:814659. [PMID: 35087767 PMCID: PMC8787120 DOI: 10.3389/fcimb.2021.814659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/13/2021] [Indexed: 02/05/2023] Open
Abstract
The human oral cavity harbors approximately 1,000 microbial species, and dysbiosis of the microflora and imbalanced microbiota-host interactions drive many oral diseases, such as dental caries and periodontal disease. Oral microbiota homeostasis is critical for systemic health. Over the last two decades, bacterial protein phosphorylation systems have been extensively studied, providing mounting evidence of the pivotal role of tyrosine and serine/threonine phosphorylation in oral bacterial dysbiosis and bacteria-host interactions. Ongoing investigations aim to discover novel kinases and phosphatases and to understand the mechanism by which these phosphorylation events regulate the pathogenicity of oral bacteria. Here, we summarize the structures of bacterial tyrosine and serine/threonine kinases and phosphatases and discuss the roles of tyrosine and serine/threonine phosphorylation systems in Porphyromonas gingivalis and Streptococcus mutans, emphasizing their involvement in bacterial metabolism and virulence, community development, and bacteria-host interactions.
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Affiliation(s)
- Liang Ren
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Daonan Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yi Ding
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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2
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Selvaraj K, Katare DP, Chand S, Chaudhary N. Trachyspermum ammi and Cinnamomum verum as nutraceuticals: Spices rich in therapeutically significant protein tyrosine phosphatases. J Food Biochem 2021; 45:e13750. [PMID: 33954990 DOI: 10.1111/jfbc.13750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/05/2021] [Accepted: 04/19/2021] [Indexed: 11/29/2022]
Abstract
Nutraceuticals need special attention as preventive molecules to create a natural barrier against various dreadful diseases like cancer and to regulate metabolism. In the present study, two spices, Trachyspermum ammi and Cinnamomum verum, been identified as excellent Protein Tyrosine Phosphatases (PTPases) sources that play significant role in the regulation of cell signal transduction and developmental processes in plants as well as animals, being lucrative and potential targets for pharmacological modulation. PTPases from both cases were partially purified into 0%-40% and 40%-80% fractions based on ammonium sulfate saturation levels. Fraction (40%-80%) exhibited a purification level of 4.44-fold and 2.86-fold with specific activity of 44.06 and 23.33 U/mg for PTPases from T. ammi and C. verum, respectively. PTPases being found to be thermally stable up to 70°C imply their industrial significance. Kinetic studies showed Km values to be 7.14 and 8.33 mM, whereas the activation energy (Ea ) values were 25.89 and 29.13 kJ/mol, respectively. Divalent cations: Cu2+ , Zn2+ , and Mn2+ acted as inhibitors of PTPases, from both sources. The Ki values of inhibitors varied from 0.014-0.125 mM in the descending order Cu2+ > Zn2+ > Mn2+ and Mn2+ > Cu2+ > Zn2+ for PTPases from T. ammi and C. verum, respectively. The inhibitory effect of sodium metavanadate aligns with prominent PTPase characteristics. In addition to these properties, the thermostability of PTPases from two spices enhances their significance in industries with therapeutically vital products. Although the source of PTPases is culinary spices, further studies are required to establish the utilization of PTPases as nutraceuticals and in therapeutic formulations. PRACTICAL APPLICATIONS: For a healthy lifestyle, awareness needs to be created by humankind towards food habits to minimize illnesses. Numerous studies have explored the consumption of nutraceutical products acts as a natural barrier and immune booster for various human ailments including SARS-COV-2. PTPases play important roles in regulating intracellular signaling and, ultimately, biological function along with their structural features. The importance of PTPases and their inhibitors has been implicated in various diseases like cancer, diabetes, and obesity. Further investigations need to be undertaken to explore the therapeutic properties of PTPases in both in vivo and in vitro for their clinical significance.
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Affiliation(s)
- Kanagarethinam Selvaraj
- Centre for Biotechnology and Biochemical Engineering, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Deepshikha Pande Katare
- Centre for Biotechnology and Biochemical Engineering, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Subhash Chand
- Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Nidhee Chaudhary
- Centre for Biotechnology and Biochemical Engineering, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
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3
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Sierra-López F, Baylón-Pacheco L, Vanegas-Villa SC, Rosales-Encina JL. Characterization of low molecular weight protein tyrosine phosphatases of Entamoeba histolytica. Biochimie 2021; 180:43-53. [PMID: 33122104 DOI: 10.1016/j.biochi.2020.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/20/2020] [Accepted: 10/24/2020] [Indexed: 12/12/2022]
Abstract
Entamoeba histolytica is an intestinal protozoan parasite of humans and is endemic in developing countries. E. histolytica has two low molecular weight protein tyrosine phosphatase (LMW-PTP) genes, EhLMW-PTP1 and EhLMW-PTP2, which are expressed in cultured trophozoites, clinical isolates, and cysts. The amino acid sequences of proteins EhLMW-PTP1 and EhLMW-PTP2 showed only one amino acid difference between them at position A85V, respectively. Both genes are expressed in cultured trophozoites, mainly EhLMW-PTP2, and in trophozoites recovered from amoebic liver abscess, the expression of EhLMW-PTP1 is downregulated. We cloned the two genes and purified the corresponding recombinant (rEhLMW-PTPs) proteins. Antibodies anti-rEhLMW-PTP2 showed that during red blood cells uptake by E. histolytica, the EhLMW-PTPs were found in the phagocytic cups based on analysis of fluorescence signals. On the other hand, rEhLMW-PTPs showed an optimum phosphatase activity at pH 6.0 with p-nitrophenyl phosphate as the substrate. They dephosphorylate phosphotyrosine and 3-O-methylfluorescein phosphate, but not phosphoserine or phosphothreonine, and the enzymatic activity is inhibited by orthovanadate. rEhLMW-PTP1 and rEhLMW-PTP2 exhibited optimum temperatures of activities at 60 °C and 58 °C, respectively, with high thermal stability at 50 °C. Also, the rEhLMW-PTPs showed high specific activities and specific km value with pNPP or OMFP as the substrates at the physiological temperature (37 °C).
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Affiliation(s)
- Francisco Sierra-López
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., Ciudad de México, Mexico.
| | - Lidia Baylón-Pacheco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., Ciudad de México, Mexico.
| | - Sonia Cynthia Vanegas-Villa
- Programa de Doctorado en Ciencias Biomédicas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de, Mexico.
| | - José Luis Rosales-Encina
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., Ciudad de México, Mexico.
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4
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Jung H, Shin SH, Kee J. Recent Updates on ProteinN‐Phosphoramidate Hydrolases. Chembiochem 2018; 20:623-633. [DOI: 10.1002/cbic.201800566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Hoyoung Jung
- Department of ChemistryUlsan National Institute of Science and Technology (UNIST) Ulsan 44919 South Korea
| | - Son Hye Shin
- Department of ChemistryUlsan National Institute of Science and Technology (UNIST) Ulsan 44919 South Korea
| | - Jung‐Min Kee
- Department of ChemistryUlsan National Institute of Science and Technology (UNIST) Ulsan 44919 South Korea
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5
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Cheung NJ, Yu W. De novo protein structure prediction using ultra-fast molecular dynamics simulation. PLoS One 2018; 13:e0205819. [PMID: 30458007 PMCID: PMC6245515 DOI: 10.1371/journal.pone.0205819] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 10/02/2018] [Indexed: 11/19/2022] Open
Abstract
Modern genomics sequencing techniques have provided a massive amount of protein sequences, but experimental endeavor in determining protein structures is largely lagging far behind the vast and unexplored sequences. Apparently, computational biology is playing a more important role in protein structure prediction than ever. Here, we present a system of de novo predictor, termed NiDelta, building on a deep convolutional neural network and statistical potential enabling molecular dynamics simulation for modeling protein tertiary structure. Combining with evolutionary-based residue-contacts, the presented predictor can predict the tertiary structures of a number of target proteins with remarkable accuracy. The proposed approach is demonstrated by calculations on a set of eighteen large proteins from different fold classes. The results show that the ultra-fast molecular dynamics simulation could dramatically reduce the gap between the sequence and its structure at atom level, and it could also present high efficiency in protein structure determination if sparse experimental data is available.
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Affiliation(s)
- Ngaam J. Cheung
- Department of Brain and Cognitive Science, DGIST, Daegu, South Korea
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Wookyung Yu
- Department of Brain and Cognitive Science, DGIST, Daegu, South Korea
- Core Protein Resources Center, DGIST, Daegu, South Korea
- * E-mail:
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Salomone-Stagni M, Musiani F, Benini S. Characterization and 1.57 Å resolution structure of the key fire blight phosphatase AmsI from Erwinia amylovora. Acta Crystallogr F Struct Biol Commun 2016; 72:903-910. [PMID: 27917839 PMCID: PMC5137468 DOI: 10.1107/s2053230x16018781] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/23/2016] [Indexed: 11/10/2022] Open
Abstract
AmsI is a low-molecular-weight protein tyrosine phosphatase that regulates the production of amylovoran in the Gram-negative bacterium Erwinia amylovora, a specific pathogen of rosaceous plants such as apple, pear and quince. Amylovoran is an exopolysaccharide that is necessary for successful infection. In order to shed light on AmsI, its structure was solved at 1.57 Å resolution at the same pH as its highest measured activity (pH 5.5). In the active site, a water molecule, bridging between the catalytic Arg15 and the reaction-product analogue sulfate, might be representative of the water molecule attacking the phospho-cysteine intermediate in the second step of the reaction mechanism.
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Affiliation(s)
- Marco Salomone-Stagni
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 5, 39100 Bolzano, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy
| | - Stefano Benini
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 5, 39100 Bolzano, Italy
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7
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Ku B, Keum CW, Lee HS, Yun HY, Shin HC, Kim BY, Kim SJ. Crystal structure of SP-PTP, a low molecular weight protein tyrosine phosphatase from Streptococcus pyogenes. Biochem Biophys Res Commun 2016; 478:1217-22. [PMID: 27545603 DOI: 10.1016/j.bbrc.2016.08.097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/17/2016] [Indexed: 11/25/2022]
Abstract
Streptococcus pyogenes, or Group A Streptococcus (GAS), is a pathogenic bacterium that causes a variety of infectious diseases. The GAS genome encodes one protein tyrosine phosphatase, SP-PTP, which plays an essential role in the replication and virulence maintenance of GAS. Herein, we present the crystal structure of SP-PTP at 1.9 Å resolution. Although SP-PTP has been reported to have dual phosphatase specificity for both phosphorylated tyrosine and serine/threonine, three-dimensional structural analysis showed that SP-PTP shares high similarity with typical low molecular weight protein tyrosine phosphatases (LMWPTPs), which are specific for phosphotyrosine, but not with dual-specificity phosphatases, in overall folding and active site composition. In the dephosphorylation activity test, SP-PTP consistently acted on phosphotyrosine substrates, but not or only minimally on phosphoserine/phosphothreonine substrates. Collectively, our structural and biochemical analyses verified SP-PTP as a canonical tyrosine-specific LMWPTP.
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Affiliation(s)
- Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; Department of Bio-Analytical Science, University of Science and Technology, Daejeon, Republic of Korea.
| | - Chae Won Keum
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; Department of Bio-Analytical Science, University of Science and Technology, Daejeon, Republic of Korea
| | - Hye Seon Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; Department of Biology, Chungnam National University, Daejeon, Republic of Korea
| | - Hye-Yeoung Yun
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; Department of Bio-Analytical Science, University of Science and Technology, Daejeon, Republic of Korea
| | - Ho-Chul Shin
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Bo Yeon Kim
- Incurable Diseases Therapeutics Research Center, World Class Institute, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongwon, Republic of Korea
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; Department of Bio-Analytical Science, University of Science and Technology, Daejeon, Republic of Korea.
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8
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Fuhrmann J, Subramanian V, Kojetin DJ, Thompson PR. Activity-Based Profiling Reveals a Regulatory Link between Oxidative Stress and Protein Arginine Phosphorylation. Cell Chem Biol 2016; 23:967-977. [PMID: 27524296 DOI: 10.1016/j.chembiol.2016.07.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/30/2016] [Accepted: 07/05/2016] [Indexed: 10/21/2022]
Abstract
Protein arginine phosphorylation is a recently discovered modification that affects multiple cellular pathways in Gram-positive bacteria. In particular, the phosphorylation of arginine residues by McsB is critical for regulating the cellular stress response. Given that the highly efficient protein arginine phosphatase YwlE prevents arginine phosphorylation under non-stress conditions, we hypothesized that this enzyme negatively regulates arginine phosphorylation and acts as a sensor of cell stress. To evaluate this hypothesis, we developed the first suite of highly potent and specific SO3-amidine-based YwlE inhibitors. With these protein arginine phosphatase-specific probes, we demonstrated that YwlE activity is suppressed by oxidative stress, which consequently increases arginine phosphorylation, thereby inducing the expression of stress-response genes, which is critical for bacterial virulence. Overall, we predict that these novel chemical tools will be widely used to study the regulation of protein arginine phosphorylation in multiple organisms.
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Affiliation(s)
- Jakob Fuhrmann
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA; Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Venkataraman Subramanian
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, MA 01605, USA; Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Douglas J Kojetin
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, MA 01605, USA; Program in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
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9
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Caselli A, Paoli P, Santi A, Mugnaioni C, Toti A, Camici G, Cirri P. Low molecular weight protein tyrosine phosphatase: Multifaceted functions of an evolutionarily conserved enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1339-55. [PMID: 27421795 DOI: 10.1016/j.bbapap.2016.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 07/05/2016] [Accepted: 07/11/2016] [Indexed: 12/31/2022]
Abstract
Originally identified as a low molecular weight acid phosphatase, LMW-PTP is actually a protein tyrosine phosphatase that acts on many phosphotyrosine-containing cellular proteins that are primarily involved in signal transduction. Differences in sequence, structure, and substrate recognition as well as in subcellular localization in different organisms enable LMW-PTP to exert many different functions. In fact, during evolution, the LMW-PTP structure adapted to perform different catalytic actions depending on the organism type. In bacteria, this enzyme is involved in the biosynthesis of group 1 and 4 capsules, but it is also a virulence factor in pathogenic strains. In yeast, LMW-PTPs dephosphorylate immunophilin Fpr3, a peptidyl-prolyl-cis-trans isomerase member of the protein chaperone family. In humans, LMW-PTP is encoded by the ACP1 gene, which is composed of three different alleles, each encoding two active enzymes produced by alternative RNA splicing. In animals, LMW-PTP dephosphorylates a number of growth factor receptors and modulates their signalling processes. The involvement of LMW-PTP in cancer progression and in insulin receptor regulation as well as its actions as a virulence factor in a number of pathogenic bacterial strains may promote the search for potent, selective and bioavailable LMW-PTP inhibitors.
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Affiliation(s)
- Anna Caselli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Viale Morgagni 50, 50134 Florence, Italy.
| | - Paolo Paoli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Viale Morgagni 50, 50134 Florence, Italy.
| | - Alice Santi
- Vascular Proteomics, Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK.
| | - Camilla Mugnaioni
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Viale Morgagni 50, 50134 Florence, Italy.
| | - Alessandra Toti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Viale Morgagni 50, 50134 Florence, Italy.
| | - Guido Camici
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Viale Morgagni 50, 50134 Florence, Italy.
| | - Paolo Cirri
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Viale Morgagni 50, 50134 Florence, Italy.
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Mijakovic I, Grangeasse C, Turgay K. Exploring the diversity of protein modifications: special bacterial phosphorylation systems. FEMS Microbiol Rev 2016; 40:398-417. [PMID: 26926353 DOI: 10.1093/femsre/fuw003] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/02/2016] [Indexed: 12/31/2022] Open
Abstract
Protein modifications not only affect protein homeostasis but can also establish new cellular protein functions and are important components of complex cellular signal sensing and transduction networks. Among these post-translational modifications, protein phosphorylation represents the one that has been most thoroughly investigated. Unlike in eukarya, a large diversity of enzyme families has been shown to phosphorylate and dephosphorylate proteins on various amino acids with different chemical properties in bacteria. In this review, after a brief overview of the known bacterial phosphorylation systems, we focus on more recently discovered and less widely known kinases and phosphatases. Namely, we describe in detail tyrosine- and arginine-phosphorylation together with some examples of unusual serine-phosphorylation systems and discuss their potential role and function in bacterial physiology, and regulatory networks. Investigating these unusual bacterial kinase and phosphatases is not only important to understand their role in bacterial physiology but will help to generally understand the full potential and evolution of protein phosphorylation for signal transduction, protein modification and homeostasis in all cellular life.
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Affiliation(s)
- Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 41296, Sweden Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Christophe Grangeasse
- Unité Microbiologie Moléculaire et Biochimie Structurale, UMR 5086-CNRS/ Université Lyon 1, Lyon 69367, France
| | - Kürşad Turgay
- Institut für Mikrobiologie, Leibniz Universität Hannover, D-30419 Hannover, Germany
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11
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Kant S, Agarwal S, Pancholi P, Pancholi V. TheStreptococcus pyogenesorphan protein tyrosine phosphatase, SP-PTP, possesses dual specificity and essential virulence regulatory functions. Mol Microbiol 2015; 97:515-40. [DOI: 10.1111/mmi.13047] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2015] [Indexed: 01/06/2023]
Affiliation(s)
- Sashi Kant
- Department of Pathology; The Ohio State University College of Medicine; Wexner Medical Center; Columbus OH USA
| | - Shivani Agarwal
- Department of Pathology; The Ohio State University College of Medicine; Wexner Medical Center; Columbus OH USA
| | - Preeti Pancholi
- Department of Pathology; The Ohio State University College of Medicine; Wexner Medical Center; Columbus OH USA
| | - Vijay Pancholi
- Department of Pathology; The Ohio State University College of Medicine; Wexner Medical Center; Columbus OH USA
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12
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Mijakovic I, Deutscher J. Protein-tyrosine phosphorylation in Bacillus subtilis: a 10-year retrospective. Front Microbiol 2015; 6:18. [PMID: 25667587 PMCID: PMC4304235 DOI: 10.3389/fmicb.2015.00018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/07/2015] [Indexed: 11/13/2022] Open
Abstract
The discovery of tyrosine-phosphorylated proteins in Bacillus subtilis in the year 2003 was followed by a decade of intensive research activity. Here we provide an overview of the lessons learned in that period. While the number of characterized kinases and phosphatases involved in reversible protein-tyrosine phosphorylation in B. subtilis has remained essentially unchanged, the number of proteins known to be targeted by this post-translational modification has increased dramatically. This is mainly due to phosphoproteomics and interactomics studies, which were instrumental in identifying new tyrosine-phosphorylated proteins. Despite their structural similarity, the two B. subtilis protein-tyrosine kinases (BY-kinases), PtkA and PtkB (EpsB), seem to accomplish different functions in the cell. The PtkB is encoded by a large operon involved in exopolysaccharide production, and its main role appears to be the control of this process. The PtkA seems to have a more complex role; it phosphorylates and regulates a large number of proteins involved in the DNA, fatty acid and carbon metabolism and engages in physical interaction with other types of kinases (Ser/Thr kinases), leading to mutual phosphorylation. PtkA also seems to respond to several activator proteins, which direct its activity toward different substrates. In that respect PtkA seems to function as a highly connected signal integration device.
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Affiliation(s)
- Ivan Mijakovic
- Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology , Göteborg, Sweden
| | - Josef Deutscher
- Centre National de la Recherche Scientifique, FRE3630 Expression Génétique Microbienne, Institut de Biologie Physico-Chimique , Paris, France ; UMR1319 Microbiologie de l'Alimentation au Service de la Santé Humaine, Institut National de la Recherche Agronomique/AgroParisTech , Jouy en Josas, France
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13
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Standish AJ, Morona R. The role of bacterial protein tyrosine phosphatases in the regulation of the biosynthesis of secreted polysaccharides. Antioxid Redox Signal 2014; 20:2274-89. [PMID: 24295407 PMCID: PMC3995119 DOI: 10.1089/ars.2013.5726] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SIGNIFICANCE Tyrosine phosphorylation and associated protein tyrosine phosphatases are gaining prominence as critical mechanisms in the regulation of fundamental processes in a wide variety of bacteria. In particular, these phosphatases have been associated with the control of the biosynthesis of capsular polysaccharides and extracellular polysaccharides, critically important virulence factors for bacteria. RECENT ADVANCES Deletion and overexpression of the phosphatases result in altered polysaccharide biosynthesis in a range of bacteria. The recent structures of associated auto-phosphorylating tyrosine kinases have suggested that the phosphatases may be critical for the cycling of the kinases between monomers and higher order oligomers. CRITICAL ISSUES Additional substrates of the phosphatases apart from cognate kinases are currently being identified. These are likely to be critical to our understanding of the mechanism by which polysaccharide biosynthesis is regulated. FUTURE DIRECTIONS Ultimately, these protein tyrosine phosphatases are an attractive target for the development of novel antimicrobials. This is particularly the case for the polymerase and histidinol phosphatase family, which is predominantly found in bacteria. Furthermore, the determination of bacterial tyrosine phosphoproteomes will likely help to uncover the fundamental roles, mechanism, and critical importance of these phosphatases in a wide range of bacteria.
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Affiliation(s)
- Alistair J Standish
- School of Molecular and Biomedical Science, University of Adelaide , Adelaide, Australia
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14
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Linford AS, Jiang NM, Edwards TE, Sherman NE, Van Voorhis WC, Stewart LJ, Myler PJ, Staker BL, Petri WA. Crystal structure and putative substrate identification for the Entamoeba histolytica low molecular weight tyrosine phosphatase. Mol Biochem Parasitol 2014; 193:33-44. [PMID: 24548880 DOI: 10.1016/j.molbiopara.2014.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 01/12/2014] [Accepted: 01/22/2014] [Indexed: 11/28/2022]
Abstract
Entamoeba histolytica is a eukaryotic intestinal parasite of humans, and is endemic in developing countries. We have characterized the E. histolytica putative low molecular weight protein tyrosine phosphatase (LMW-PTP). The structure for this amebic tyrosine phosphatase was solved, showing the ligand-induced conformational changes necessary for binding of substrate. In amebae, it was expressed at low but detectable levels as detected by immunoprecipitation followed by immunoblotting. A mutant LMW-PTP protein in which the catalytic cysteine in the active site was replaced with a serine lacked phosphatase activity, and was used to identify a number of trapped putative substrate proteins via mass spectrometry analysis. Seven of these putative substrate protein genes were cloned with an epitope tag and overexpressed in amebae. Five of these seven putative substrate proteins were demonstrated to interact specifically with the mutant LMW-PTP. This is the first biochemical study of a small tyrosine phosphatase in Entamoeba, and sets the stage for understanding its role in amebic biology and pathogenesis.
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Affiliation(s)
- Alicia S Linford
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA.
| | - Nona M Jiang
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - Nicholas E Sherman
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Lance J Stewart
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Seattle Biomedical Research Institute, Seattle, WA 98109, USA; Departments of Global Health and Medical Education & Biomedical Informatics, University of Washington, Seattle, WA 98195, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA; Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA.
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15
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Mori Y, Kimura Y. Myxococcus xanthus low-molecular-weight protein tyrosine phosphatase homolog, ArsA, possesses arsenate reductase activity. J Biosci Bioeng 2014; 118:10-3. [PMID: 24503422 DOI: 10.1016/j.jbiosc.2013.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 11/25/2022]
Abstract
Myxococcus xanthus MXAN_0575, ArsA, exhibited sequence homology to low-molecular-weight protein tyrosine phosphatases (LMWPTPs) and arsenate reductases. ArsA exhibited weak phosphatase activity toward p-nitrophenyl phosphate, and high arsenate reductase activity, suggesting that ArsA may play a role in arsenate reductase, but not LMWPTP.
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Affiliation(s)
- Yumi Mori
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Yoshio Kimura
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan.
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16
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Gulerez IE, Gehring K. X-ray crystallography and NMR as tools for the study of protein tyrosine phosphatases. Methods 2014; 65:175-83. [DOI: 10.1016/j.ymeth.2013.07.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/19/2013] [Accepted: 07/23/2013] [Indexed: 10/26/2022] Open
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17
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Fuhrmann J, Subramanian V, Thompson PR. Targeting the arginine phosphatase YwlE with a catalytic redox-based inhibitor. ACS Chem Biol 2013; 8:2024-32. [PMID: 23838530 DOI: 10.1021/cb4001469] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein phosphatases are critical regulators of cellular signaling in both eukaryotes and prokaryotes. The majority of protein phosphatases dephosphorylate phosphoserine/phosphothreonine or phosphotyrosine residues. Recently, however, YwlE, a member of the low-molecular weight protein tyrosine phosphatase (LMW-PTP) family, was shown to efficiently target phosphoarginine. YwlE shares several sequence motifs with this family including the C(X)4 CR(S/T) motif that is crucial for catalysis and redox regulation of the enzyme. Herein we confirm that Cys9 and Cys14 play important roles in YwlE catalysis and regulation. On the basis of these observations, we designed and synthesized a YwlE inhibitor, denoted cyc-SeCN-amidine, that irreversibly inhibits YwlE (kinact/KI = 310 M(-1) min(-1)) by inducing disulfide bond formation between the two active site cysteine residues. Interestingly, inactivation appears to be catalytic, since the compound is neither destroyed nor altered after enzyme inhibition. Although the exact mechanism of disulfide induction remains elusive, we propose several potential mechanisms accounting for the cyc-SeCN-amidine mediated inhibition of YwlE. These findings could stimulate the design of similar selenium-based compounds targeting other redox-sensitive enzymes.
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Affiliation(s)
- Jakob Fuhrmann
- Department
of Chemistry and ‡The Kellogg School of Science and Technology, The Scripps Research Institute, 130 Scripps Way, Jupiter,
Florida 33458, United States
| | - Venkataraman Subramanian
- Department
of Chemistry and ‡The Kellogg School of Science and Technology, The Scripps Research Institute, 130 Scripps Way, Jupiter,
Florida 33458, United States
| | - Paul R. Thompson
- Department
of Chemistry and ‡The Kellogg School of Science and Technology, The Scripps Research Institute, 130 Scripps Way, Jupiter,
Florida 33458, United States
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18
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Fuhrmann J, Mierzwa B, Trentini D, Spiess S, Lehner A, Charpentier E, Clausen T. Structural Basis for Recognizing Phosphoarginine and Evolving Residue-Specific Protein Phosphatases in Gram-Positive Bacteria. Cell Rep 2013; 3:1832-9. [DOI: 10.1016/j.celrep.2013.05.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/07/2013] [Accepted: 05/10/2013] [Indexed: 12/31/2022] Open
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19
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Protein Functional Dynamics in Multiple Timescales as Studied by NMR Spectroscopy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:219-51. [DOI: 10.1016/b978-0-12-411636-8.00006-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
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20
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Matiollo C, Ecco G, Menegatti ACO, Razzera G, Vernal J, Terenzi H. S-nitrosylation of Mycobacterium tuberculosis tyrosine phosphatase A (PtpA) induces its structural instability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:191-6. [PMID: 23102706 DOI: 10.1016/j.bbapap.2012.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 10/04/2012] [Accepted: 10/07/2012] [Indexed: 02/06/2023]
Abstract
S-nitrosylation is associated with signal transduction and microbicidal activity of nitric oxide (NO). We have recently described the S-nitrosylation of Mycobacterium tuberculosis protein tyrosine phosphatase A, PtpA, an enzyme that plays an important role in mycobacteria survival inside macrophages. This post-translational modification decreases the activity of the enzyme upon modification of a single Cys residue, C53. The aim of the present work was the investigation of the effect of S-nitrosylation in PtpA kinetic parameters, thermal stability and structure. It was observed that the K(M) of nitrosylated PtpA was similar to its unmodified form, but the V(max) was significantly reduced. In contrast, treatment of PtpA C53A with GSNO, did not alter either K(M) or V(max). These results confirmed that PtpA S-nitrosylation occurs specifically in the non-catalytic C53 and that this modification does not affect substrate affinity. Using circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy techniques it was shown that PtpA S-nitrosylation decreased protein thermal stability and promoted a local effect in the surroundings of the C53 residue, which interfered in both protein stability and function.
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Affiliation(s)
- Camila Matiollo
- Centro de Biologia Molecular Estrutural-INBEB, Departamento de Bioquímica, CCB, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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21
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Stehle T, Sreeramulu S, Löhr F, Richter C, Saxena K, Jonker HRA, Schwalbe H. The apo-structure of the low molecular weight protein-tyrosine phosphatase A (MptpA) from Mycobacterium tuberculosis allows for better target-specific drug development. J Biol Chem 2012; 287:34569-82. [PMID: 22888002 DOI: 10.1074/jbc.m112.399261] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Protein-tyrosine phosphatases (PTPs) and protein-tyrosine kinases co-regulate cellular processes. In pathogenic bacteria, they are frequently exploited to act as key virulence factors for human diseases. Mycobacterium tuberculosis, the causative organism of tuberculosis, secretes a low molecular weight PTP (LMW-PTP), MptpA, which is required for its survival upon infection of host macrophages. Although there is otherwise no sequence similarity of LMW-PTPs to other classes of PTPs, the phosphate binding loop (P-loop) CX(5)R and the loop containing a critical aspartic acid residue (D-loop), required for the catalytic activity, are well conserved. In most high molecular weight PTPs, ligand binding to the P-loop triggers a large conformational reorientation of the D-loop, in which it moves ∼10 Å, from an "open" to a "closed" conformation. Until now, there have been no ligand-free structures of LMW-PTPs described, and hence the dynamics of the D-loop have remained largely unknown for these PTPs. Here, we present a high resolution solution NMR structure of the free form of the MptpA LMW-PTP. In the absence of ligand and phosphate ions, the D-loop adopts an open conformation. Furthermore, we characterized the binding site of phosphate, a competitive inhibitor of LMW-PTPs, on MptpA and elucidated the involvement of both the P- and D-loop in phosphate binding. Notably, in LMW-PTPs, the phosphorylation status of two well conserved tyrosine residues, typically located in the D-loop, regulates the enzyme activity. PtkA, the kinase complementary to MptpA, phosphorylates these two tyrosine residues in MptpA. We characterized the MptpA-PtkA interaction by NMR spectroscopy to show that both the P- and D-loop form part of the binding interface.
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Affiliation(s)
- Tanja Stehle
- Institute for Organic Chemistry and Chemical Biology, ohann Wolfgang Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
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22
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New strategies in fighting TB: targeting Mycobacterium tuberculosis-secreted phosphatases MptpA & MptpB. Future Med Chem 2010; 2:1325-37. [DOI: 10.4155/fmc.10.214] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Mycobacterium tuberculosis is the most successful human pathogen due to its ability to challenge the innate immune system and survive in the infected host for a lifetime. Although tuberculosis (TB) is a curable disease, severe multidrug resistance to traditional antibiotics has caused a resurgence of the infection worldwide. The secreted phosphatases MptpA and MptpB are key virulence factors that play important roles in survival of M. tuberculosis during macrophage infection. These enzymes are therefore attractive alternative targets for chemotherapy. In this review we analyze the structural features that characterize these two phosphatases and differentiate them from human homologs. Their structural peculiarities are important for drug-design considerations and the future development of selective inhibitors. We describe the recent efforts in developing specific, selective and cell-active inhibitors of MptpA and MptpB, and discuss their potential applications as alternative treatments of TB.
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23
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Wen Y, Li J, Yao W, Xiong M, Hong J, Peng Y, Xiao G, Lin D. Unique structural characteristics of the rabbit prion protein. J Biol Chem 2010; 285:31682-93. [PMID: 20639199 DOI: 10.1074/jbc.m110.118844] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rabbits are one of the few mammalian species that appear to be resistant to transmissible spongiform encephalopathies due to the structural characteristics of the rabbit prion protein (RaPrP(C)) itself. Here, we determined the solution structures of the recombinant protein RaPrP(C)-(91-228) and its S173N variant and detected the backbone dynamics of their structured C-terminal domains-(121-228). In contrast to many other mammalian PrP(C)s, loop 165-172, which connects β-sheet-2 and α-helix-2, is well-defined in RaPrP(C). For the first time, order parameters S(2) are obtained for residues in this loop region, indicating that loop 165-172 of RaPrP(C) is highly ordered. Compared with the wild-type RaPrP(C), less hydrogen bonds form in the S173N variant. The NMR dynamics analysis reveals a distinct increase in the structural flexibility of loop 165-172 and helix-3 after the S173N substitution, implying that the S173N substitution disturbs the long range interaction of loop 165-172 with helix-3, which further leads to a marked decrease in the global conformational stability. Significantly, RaPrP(C) possesses a unique charge distribution, carrying a continuous area of positive charges on the surface, which is distinguished from other PrP(C)s. The S173N substitution causes visible changes of the charge distribution around the recognition sites for the hypothetical protein X. Our results suggest that the ordered loop 165-172 and its interaction with helix-3, together with the unique distribution of surface electrostatic potential, significantly contribute to the unique structural characteristics of RaPrP(C).
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Affiliation(s)
- Yi Wen
- NMR Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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24
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Hu J, Li D, Su XD, Jin C, Xia B. Solution structure and conformational heterogeneity of acylphosphatase from Bacillus subtilis. FEBS Lett 2010; 584:2852-6. [PMID: 20447399 DOI: 10.1016/j.febslet.2010.04.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 04/26/2010] [Accepted: 04/26/2010] [Indexed: 10/19/2022]
Abstract
Acylphosphatase is a small enzyme that catalyzes the hydrolysis of acyl phosphates. Here, we present the solution structure of acylphosphatase from Bacillus subtilis (BsAcP), the first from a Gram-positive bacterium. We found that its active site is disordered, whereas it converted to an ordered state upon ligand binding. The structure of BsAcP is sensitive to pH and it has multiple conformations in equilibrium at acidic pH (pH<5.8). Only one main conformation could bind ligand, and the relative population of these states is modulated by ligand concentration. This study provides direct evidence for the role of ligand in conformational selection.
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Affiliation(s)
- Jicheng Hu
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, China
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25
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Blobel J, Bernadó P, Xu H, Jin C, Pons M. Weak oligomerization of low-molecular-weight protein tyrosine phosphatase is conserved from mammals to bacteria. FEBS J 2009; 276:4346-57. [PMID: 19678837 DOI: 10.1111/j.1742-4658.2009.07139.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The well-characterized self-association of a mammalian low-molecular-weight protein tyrosine phosphatase (lmwPTP) produces inactive oligomers that are in equilibrium with active monomers. A role of the inactive oligomers as supramolecular proenzymes has been suggested. The oligomerization equilibrium of YwlE, a lmwPTP from Bacillus subtilis, was studied by NMR. Chemical shift data and NMR relaxation confirm that dimerization takes place through the enzyme's active site, and is fully equivalent to the dimerization previously characterized in a eukaryotic low-molecular-weight phosphatase, with similarly large dissociation constants. The similarity between the oligomerization of prokaryotic and eukaryotic phosphatases extends beyond the dimer and involves higher order oligomers detected by NMR relaxation analysis at high protein concentrations. The conservation across different kingdoms of life suggests a physiological role for lmwPTP oligomerization in spite of the weak association observed in vitro. Structural data suggest that substrate modulation of the oligomerization equilibrium could be a regulatory mechanism leading to the generation of signaling pulses. The presence of a phenylalanine residue in the dimerization site of YwlE, replacing a tyrosine residue conserved in all eukaryotic lmwPTPs, demonstrates that lmwPTP regulation by oligomerization can be independent from tyrosine phosphorylation.
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Affiliation(s)
- Jascha Blobel
- Laboratory of Biomolecular NMR, Institute for Research in Biomedicine, Barcelona, Spain
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26
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Hagelueken G, Huang H, Mainprize IL, Whitfield C, Naismith JH. Crystal structures of Wzb of Escherichia coli and CpsB of Streptococcus pneumoniae, representatives of two families of tyrosine phosphatases that regulate capsule assembly. J Mol Biol 2009; 392:678-88. [PMID: 19616007 PMCID: PMC2777267 DOI: 10.1016/j.jmb.2009.07.026] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/07/2009] [Accepted: 07/09/2009] [Indexed: 12/11/2022]
Abstract
Many Gram-positive and Gram-negative bacteria utilize polysaccharide surface layers called capsules to evade the immune system; consequently, the synthesis and export of the capsule are a potential therapeutic target. In Escherichia coli K-30, the integral membrane tyrosine autokinase Wzc and the cognate phosphatase Wzb have been shown to be key for both synthesis and assembly of capsular polysaccharides. In the Gram-positive bacterium Streptococcus pneumoniae, the CpsCD complex is analogous to Wzc and the phosphatase CpsB is the corresponding cognate phosphatase. The phosphatases are known to dephosphorylate their corresponding autokinases, yet despite their functional equivalence, they share no sequence homology. We present the structure of Wzb in complex with phosphate and high-resolution structures of apo-CpsB and a phosphate-complexed CpsB. We show that both proteins are active toward Wzc and thereby demonstrate that CpsB is not specific for CpsCD. CpsB is a novel enzyme and represents the first solved structure of a tyrosine phosphatase from a Gram-positive bacterium. Wzb and CpsB have completely different structures, suggesting that they must operate by very different mechanisms. Although the mechanism of Wzb can be inferred from previous studies, CpsB appears to have a tyrosine phosphatase mechanism not observed before. We propose a chemical mechanism for CpsB based on site-directed mutagenesis and structural data.
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Affiliation(s)
- Gregor Hagelueken
- Centre for Biomolecular Sciences, The University of St. Andrews, Fife KY16 9RH, UK
| | - Hexian Huang
- Centre for Biomolecular Sciences, The University of St. Andrews, Fife KY16 9RH, UK
| | - Iain L. Mainprize
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - James H. Naismith
- Centre for Biomolecular Sciences, The University of St. Andrews, Fife KY16 9RH, UK
- Corresponding author.
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27
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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: 111] [Impact Index Per Article: 6.9] [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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28
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Tolkatchev D, Shaykhutdinov R, Xu P, Plamondon J, Watson DC, Young NM, Ni F. Three-dimensional structure and ligand interactions of the low molecular weight protein tyrosine phosphatase from Campylobacter jejuni. Protein Sci 2007; 15:2381-94. [PMID: 17008719 PMCID: PMC2242389 DOI: 10.1110/ps.062279806] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A putative low molecular weight protein tyrosine phosphatase (LMW-PTP) was identified in the genome sequence of the bacterial pathogen, Campylobacter jejuni. This novel gene, cj1258, has sequence homology with a distinctive class of phosphatases widely distributed among prokaryotes and eukaryotes. We report here the solution structure of Cj1258 established by high-resolution NMR spectroscopy using NOE-derived distance restraints, hydrogen bond data, and torsion angle restraints. The three-dimensional structure consists of a central four-stranded parallel beta-sheet flanked by five alpha-helices, revealing an overall structural topology similar to those of the eukaryotic LMW-PTPs, such as human HCPTP-A, bovine BPTP, and Saccharomyces cerevisiae LTP1, and to those of the bacterial LMW-PTPs MPtpA from Mycobacterium tuberculosis and YwlE from Bacillus subtilis. The active site of the enzyme is flexible in solution and readily adapts to the binding of ligands, such as the phosphate ion. An NMR-based screen was carried out against a number of potential inhibitors and activators, including phosphonomethylphenylalanine, derivatives of the cinnamic acid, 2-hydroxy-5-nitrobenzaldehyde, cinnamaldehyde, adenine, and hypoxanthine. Despite its bacterial origin, both the three-dimensional structure and ligand-binding properties of Cj1258 suggest that this novel phosphatase may have functional roles close to those of eukaryotic and mammalian tyrosine phosphatases. The three-dimensional structure along with mapping of small-molecule binding will be discussed in the context of developing high-affinity inhibitors of this novel LMW-PTP.
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Affiliation(s)
- Dmitri Tolkatchev
- Biomolecular NMR and Protein Research Group, Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2, Canada
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29
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Lescop E, Hu Y, Xu H, Hu W, Chen J, Xia B, Jin C. The solution structure of Escherichia coli Wzb reveals a novel substrate recognition mechanism of prokaryotic low molecular weight protein-tyrosine phosphatases. J Biol Chem 2006; 281:19570-7. [PMID: 16651264 DOI: 10.1074/jbc.m601263200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Low molecular weight protein-tyrosine phosphatases (LMW-PTPs) are small enzymes that ubiquitously exist in various organisms and play important roles in many biological processes. In Escherichia coli, the LMW-PTP Wzb dephosphorylates the autokinase Wzc, and the Wzc/Wzb pair regulates colanic acid production. However, the substrate recognition mechanism of Wzb is still poorly understood thus far. To elucidate the molecular basis of the catalytic mechanism, we have determined the solution structure of Wzb at high resolution by NMR spectroscopy. The Wzb structure highly resembles that of the typical LMW-PTP fold, suggesting that Wzb may adopt a similar catalytic mechanism with other LMW-PTPs. Nevertheless, in comparison with eukaryotic LMW-PTPs, the absence of an aromatic amino acid at the bottom of the active site significantly alters the molecular surface and implicates Wzb may adopt a novel substrate recognition mechanism. Furthermore, a structure-based multiple sequence alignment suggests that a class of the prokaryotic LMW-PTPs may share a similar substrate recognition mechanism with Wzb. The current studies provide the structural basis for rational drug design against the pathogenic bacteria.
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Affiliation(s)
- Ewen Lescop
- Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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