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Szabó JE, Németh V, Papp-Kádár V, Nyíri K, Leveles I, Bendes AÁ, Zagyva I, Róna G, Pálinkás HL, Besztercei B, Ozohanics O, Vékey K, Liliom K, Tóth J, Vértessy BG. Highly potent dUTPase inhibition by a bacterial repressor protein reveals a novel mechanism for gene expression control. Nucleic Acids Res 2014; 42:11912-20. [PMID: 25274731 PMCID: PMC4231751 DOI: 10.1093/nar/gku882] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transfer of phage-related pathogenicity islands of Staphylococcus aureus (SaPI-s) was recently reported to be activated by helper phage dUTPases. This is a novel function for dUTPases otherwise involved in preservation of genomic integrity by sanitizing the dNTP pool. Here we investigated the molecular mechanism of the dUTPase-induced gene expression control using direct techniques. The expression of SaPI transfer initiating proteins is repressed by proteins called Stl. We found that Φ11 helper phage dUTPase eliminates SaPIbov1 Stl binding to its cognate DNA by binding tightly to Stl protein. We also show that dUTPase enzymatic activity is strongly inhibited in the dUTPase:Stl complex and that the dUTPase:dUTP complex is inaccessible to the Stl repressor. Our results disprove the previously proposed G-protein-like mechanism of SaPI transfer activation. We propose that the transfer only occurs if dUTP is cleared from the nucleotide pool, a condition promoting genomic stability of the virulence elements.
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Affiliation(s)
- Judit E Szabó
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Veronika Németh
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Veronika Papp-Kádár
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Kinga Nyíri
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Ibolya Leveles
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Abris Á Bendes
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Imre Zagyva
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Gergely Róna
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Hajnalka L Pálinkás
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Balázs Besztercei
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Olivér Ozohanics
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Károly Vékey
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Károly Liliom
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Judit Tóth
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Beáta G Vértessy
- Institutes of Enzymology and Organic Chemistry, RCNS, Hungarian Academy of Sciences, Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
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18
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Barabás O, Németh V, Bodor A, Perczel A, Rosta E, Kele Z, Zagyva I, Szabadka Z, Grolmusz VI, Wilmanns M, Vértessy BG. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling. Nucleic Acids Res 2013; 41:10542-55. [PMID: 23982515 PMCID: PMC3905902 DOI: 10.1093/nar/gkt756] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 12/26/2022] Open
Abstract
Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason-Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy ((31)P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme-product complex structure.
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Affiliation(s)
- Orsolya Barabás
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Veronika Németh
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Andrea Bodor
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - András Perczel
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Edina Rosta
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Zoltán Kele
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Imre Zagyva
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Zoltán Szabadka
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Vince I. Grolmusz
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Matthias Wilmanns
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Beáta G. Vértessy
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
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