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Albani S, Polsinelli I, Mazzei L, Musiani F, Benini S. Determination and Kinetic Characterization of a New Potential Inhibitor for AmsI Protein Tyrosine Phosphatase from the Apple Pathogen Erwinia amylovora. Molecules 2023; 28:7774. [PMID: 38067503 PMCID: PMC10708540 DOI: 10.3390/molecules28237774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Erwinia amylovora is a Gram-negative bacterium, responsible for the fire blight disease in Rosaceae plants. Its virulence is correlated with the production of an exopolysaccharide (EPS) called amylovoran, which protects the bacterium from the surrounding environment and helps its diffusion inside the host. Amylovoran biosynthesis relies on the expression of twelve genes clustered in the ams operon. One of these genes, amsI, encodes for a Low Molecular Weight Protein Tyrosine Phosphatase (LMW-PTP) called EaAmsI, which plays a key role in the regulation of the EPS production pathway. For this reason, EaAmsI was chosen in this work as a target for the development of new antibacterial agents against E. amylovora. To achieve this aim, a set of programs (DOCK6, OpenEye FRED) was selected to perform a virtual screening using a database of ca. 700 molecules. The six best-scoring compounds identified were tested in in vitro assays. A complete inhibition kinetic characterization carried out on the most promising molecule (n-Heptyl β-D-glucopyranoside, N7G) showed an inhibition constant of 7.8 ± 0.6 µM. This study represents an initial step towards the development of new EaAmsI inhibitors able to act as antibacterial agents against E. amylovora infections.
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Affiliation(s)
- Simone Albani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (S.A.); (L.M.)
| | - Ivan Polsinelli
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl), Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, 39100 Bolzano, Italy;
- Institute of Molecular and Translational Cardiology (IMTC), IRCCS Policlinico San Donato, 20097 San Donato Milanese, Italy
| | - Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (S.A.); (L.M.)
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (S.A.); (L.M.)
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl), Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, 39100 Bolzano, Italy;
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Abstract
All currently known architectures of outer-membrane beta barrels (OMBBs) have only one barrel. While the vast majority function as oligomers, with barrels from different chains packing against each other in the membrane, it was assumed that these multiple chains are needed to form multibarrel structures. And yet, here we show that multibarrel chains exist. Using state-of-the-art sequence and structure analysis tools, we report the discovery of more than 30 multibarrel architectures from gram-negative bacteria. The discovery of these architectures reveals another interesting chapter in OMBB evolution and has implications for protein engineering. The evolutionary advantages of multibarrels are yet to be discovered. Outer-membrane beta barrels (OMBBs) are found in the outer membrane of gram-negative bacteria and eukaryotic organelles. OMBBs fold as antiparallel β-sheets that close onto themselves, forming pores that traverse the membrane. Currently known structures include only one barrel, of 8 to 36 strands, per chain. The lack of multi-OMBB chains is surprising, as most OMBBs form oligomers, and some function only in this state. Using a combination of sensitive sequence comparison methods and coevolutionary analysis tools, we identify many proteins combining multiple beta barrels within a single chain; combinations that include eight-stranded barrels prevail. These multibarrels seem to be the result of independent, lineage-specific fusion and amplification events. The absence of multibarrels that are universally conserved in bacteria with an outer membrane, coupled with their frequent de novo genesis, suggests that their functions are not essential but rather beneficial in specific environments. Adjacent barrels of complementary function within the same chain may allow for functions beyond those of the individual barrels.
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Wang X, Ma Q. Wzb of Vibrio vulnificus represents a new group of low-molecular-weight protein tyrosine phosphatases with a unique insertion in the W-loop. J Biol Chem 2021; 296:100280. [PMID: 33450227 PMCID: PMC7948962 DOI: 10.1016/j.jbc.2021.100280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/28/2020] [Accepted: 01/08/2021] [Indexed: 12/23/2022] Open
Abstract
Protein tyrosine phosphorylation regulates the production of capsular polysaccharide, an essential virulence factor of the deadly pathogen Vibrio vulnificus. The process requires the protein tyrosine kinase Wzc and its cognate phosphatase Wzb, both of which are largely uncharacterized. Herein, we report the structures of Wzb of V. vulnificus (VvWzb) in free and ligand-bound forms. VvWzb belongs to the low-molecular-weight protein tyrosine phosphatase (LMWPTP) family. Interestingly, it contains an extra four-residue insertion in the W-loop, distinct from all known LMWPTPs. The W-loop of VvWzb protrudes from the protein body in the free structure, but undergoes significant conformational changes to fold toward the active site upon ligand binding. Deleting the four-residue insertion from the W-loop severely impaired the enzymatic activity of VvWzb, indicating its importance for optimal catalysis. However, mutating individual residues or even substituting the whole insertion with four alanine residues only modestly decreased the enzymatic activity, suggesting that the contribution of the insertion to catalysis is not determined by the sequence specificity. Furthermore, inserting the four residues into Escherichia coli Wzb at the corresponding position enhanced its activity as well, indicating that the four-residue insertion in the W-loop can act as a general activity enhancing element for other LMWPTPs. The novel W-loop type and phylogenetic analysis suggested that VvWzb and its homologs should be classified into a new group of LMWPTPs. Our study sheds new insight into the catalytic mechanism and structural diversity of the LMWPTP family and promotes the understanding of the protein tyrosine phosphorylation system in prokaryotes.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qingjun Ma
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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Ahmad Z, Morona R, Standish AJ. In vitro characterization and identification of potential substrates of a low molecular weight protein tyrosine phosphatase in Streptococcus pneumoniae. MICROBIOLOGY-SGM 2018; 164:697-703. [PMID: 29485030 DOI: 10.1099/mic.0.000631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Streptococcus pneumoniae is a major human pathogen responsible for significant mortality and morbidity worldwide. Within the annotated genome of the pneumococcus lies a previously uncharacterized protein tyrosine phosphatase which shows homology to low molecular weight protein tyrosine phosphatases (LMWPTPs). LMWPTPs modulate many processes critical for the pathogenicity of a number of bacteria including capsular polysaccharide biosynthesis, stress response and persistence in host macrophages. Here, we demonstrate that Spd1837 is indeed a LMWPTP, by purifying the protein, and characterizing its phosphatase activity. Spd1837 showed specific tyrosine phosphatase activity, and it did not form higher order oligomers in contrast to many other LMWPTPs. Substrate-trapping assays using the wild-type and the phosphatase-deficient Spd1837 identified potential substrates/interacting proteins including major metabolic enzymes such as ATP-dependent-6-phosphofructokinase and Hpr kinase/phosphorylase. Given the tight association between the bacterial basic physiology and virulence, this study hopes to prompt further investigation of how the pneumococcus controls its metabolic flux via the LMWPTP Spd1837.
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Affiliation(s)
- Zuleeza Ahmad
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, 5005 South Australia, Australia
| | - Renato Morona
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, 5005 South Australia, Australia
| | - Alistair J Standish
- Research Centre for Infectious Diseases, Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, 5005 South Australia, Australia
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Bertoldo JB, Rodrigues T, Dunsmore L, Aprile FA, Marques MC, Rosado LA, Boutureira O, Steinbrecher TB, Sherman W, Corzana F, Terenzi H, Bernardes GJL. A Water-Bridged Cysteine-Cysteine Redox Regulation Mechanism in Bacterial Protein Tyrosine Phosphatases. Chem 2017; 3:665-677. [PMID: 29094109 PMCID: PMC5656095 DOI: 10.1016/j.chempr.2017.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 06/01/2017] [Accepted: 07/07/2017] [Indexed: 11/25/2022]
Abstract
The emergence of multidrug-resistant Mycobacterium tuberculosis (Mtb) strains highlights the need to develop more efficacious and potent drugs. However, this goal is dependent on a comprehensive understanding of Mtb virulence protein effectors at the molecular level. Here, we used a post-expression cysteine (Cys)-to-dehydrolanine (Dha) chemical editing strategy to identify a water-mediated motif that modulates accessibility of the protein tyrosine phosphatase A (PtpA) catalytic pocket. Importantly, this water-mediated Cys-Cys non-covalent motif is also present in the phosphatase SptpA from Staphylococcus aureus, which suggests a potentially preserved structural feature among bacterial tyrosine phosphatases. The identification of this structural water provides insight into the known resistance of Mtb PtpA to the oxidative conditions that prevail within an infected host macrophage. This strategy could be applied to extend the understanding of the dynamics and function(s) of proteins in their native state and ultimately aid in the design of small-molecule modulators.
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Affiliation(s)
- Jean B Bertoldo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.,Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Lavinia Dunsmore
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Marta C Marques
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Leonardo A Rosado
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Omar Boutureira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | - Woody Sherman
- Schrödinger, 120 West 45th Street, New York, NY 10036, USA
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006 Logroño, Spain
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
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Benini S, Toccafondi M, Rejzek M, Musiani F, Wagstaff BA, Wuerges J, Cianci M, Field RA. Glucose-1-phosphate uridylyltransferase from Erwinia amylovora: Activity, structure and substrate specificity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1348-1357. [PMID: 28844747 DOI: 10.1016/j.bbapap.2017.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 08/05/2017] [Accepted: 08/09/2017] [Indexed: 10/19/2022]
Abstract
Erwinia amylovora, a Gram-negative plant pathogen, is the causal agent of Fire Blight, a contagious necrotic disease affecting plants belonging to the Rosaceae family, including apple and pear. E. amylovora is highly virulent and capable of rapid dissemination in orchards; effective control methods are still lacking. One of its most important pathogenicity factors is the exopolysaccharide amylovoran. Amylovoran is a branched polymer made by the repetition of units mainly composed of galactose, with some residues of glucose, glucuronic acid and pyruvate. E. amylovora glucose-1-phosphate uridylyltransferase (UDP-glucose pyrophosphorylase, EC 2.7.7.9) has a key role in amylovoran biosynthesis. This enzyme catalyses the production of UDP-glucose from glucose-1-phosphate and UTP, which the epimerase GalE converts into UDP-galactose, the main building block of amylovoran. We determined EaGalU kinetic parameters and substrate specificity with a range of sugar 1-phosphates. At time point 120min the enzyme catalysed conversion of the sugar 1-phosphate into the corresponding UDP-sugar reached 74% for N-acetyl-α-d-glucosamine 1-phosphate, 28% for α-d-galactose 1-phosphate, 0% for α-d-galactosamine 1-phosphate, 100% for α-d-xylose 1-phosphate, 100% for α-d-glucosamine 1-phosphate, 70% for α-d-mannose 1-phosphate, and 0% for α-d-galacturonic acid 1-phosphate. To explain our results we obtained the crystal structure of EaGalU and augmented our study by docking the different sugar 1-phosphates into EaGalU active site, providing both reliable models for substrate binding and enzyme specificity, and a rationale that explains the different activity of EaGalU on the sugar 1-phosphates used. These data demonstrate EaGalU potential as a biocatalyst for biotechnological purposes, as an alternative to the enzyme from Escherichia coli, besides playing an important role in E. amylovora pathogenicity.
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Affiliation(s)
- Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, 39100 Bolzano, Italy.
| | - Mirco Toccafondi
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, 39100 Bolzano, Italy
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna 40127, Italy
| | - Ben A Wagstaff
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jochen Wuerges
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, 39100 Bolzano, Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Universita' Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy; Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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