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Takahashi DT, Gadelle D, Agama K, Kiselev E, Zhang H, Yab E, Petrella S, Forterre P, Pommier Y, Mayer C. Topoisomerase I (TOP1) dynamics: conformational transition from open to closed states. Nat Commun 2022; 13:59. [PMID: 35013228 PMCID: PMC8748870 DOI: 10.1038/s41467-021-27686-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022] Open
Abstract
Eukaryotic topoisomerases I (TOP1) are ubiquitous enzymes removing DNA torsional stress. However, there is little data concerning the three-dimensional structure of TOP1 in the absence of DNA, nor how the DNA molecule can enter/exit its closed conformation. Here, we solved the structure of thermostable archaeal Caldiarchaeum subterraneum CsTOP1 in an apo-form. The enzyme displays an open conformation resulting from one substantial rotation between the capping (CAP) and the catalytic (CAT) modules. The junction between these two modules is a five-residue loop, the hinge, whose flexibility permits the opening/closing of the enzyme and the entry of DNA. We identified a highly conserved tyrosine near the hinge as mediating the transition from the open to closed conformation upon DNA binding. Directed mutagenesis confirmed the importance of the hinge flexibility, and linked the enzyme dynamics with sensitivity to camptothecin, a TOP1 inhibitor targeting the TOP1 enzyme catalytic site in the closed conformation. Topoisomerase I (TOP1) relaxes both positive and negative supercoils by nicking DNA and after rotation of the broken DNA strand closes the nick. Here, the authors present the DNA free crystal structure of TOP1 from the hyperthermophilic archaeon Caldiarchaeum subterraneum in the open form and discuss the mechanism of how DNA enters the catalytic site of TOP1.
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Affiliation(s)
- Diane T Takahashi
- Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, Cedex, France. .,Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France. .,Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR 7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, BP 10413, F-67412, Illkirch, France.
| | - Danièle Gadelle
- Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, Cedex, France
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Evgeny Kiselev
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Emilie Yab
- Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Stephanie Petrella
- Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Patrick Forterre
- Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, Cedex, France
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA.
| | - Claudine Mayer
- Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France.,Université de Paris, F-75013, Paris, France.,ICube-UMR7357, CSTB, Centre de Recherche en Biomédecine de Strasbourg, 67084, Strasbourg, France
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2
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Affiliation(s)
- Giovanni Capranico
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Jessica Marinello
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Giovanni Chillemi
- SCAI
SuperComputing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185 Rome, Italy
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Vutey V, Castelli S, D'Annessa I, Sâmia LBP, Souza-Fagundes EM, Beraldo H, Desideri A. Human topoisomerase IB is a target of a thiosemicarbazone copper(II) complex. Arch Biochem Biophys 2016; 606:34-40. [PMID: 27431056 DOI: 10.1016/j.abb.2016.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/30/2016] [Accepted: 07/12/2016] [Indexed: 02/03/2023]
Abstract
The human topoisomerase IB inhibition and the antiproliferative activity of 3-(4-bromophenyl)-1-pyridin-2-ylprop-2-en-1-one thiosemicarbazone HPyCT4BrPh alone and its copper(II) complex [Cu(PyCT4BrPh)Cl] was investigated. [Cu(PyCT4BrPh)Cl] inhibits both the DNA cleavage and religation step of the enzyme, whilst the ligand alone does not display any effect. In addition we show that coordination to copper(II) improves the cytotoxicity of HPyCT4BrPh against THP-1 leukemia and MCF-7 breast cancer cells. The data indicate that the copper(II) thiosemicarbazone complex may hit human topoisomerase IB and that metal coordination can be useful to improve cytotoxicity of this versatile class of compounds.
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Affiliation(s)
- Venn Vutey
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Castelli
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Ilda D'Annessa
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Luciana B P Sâmia
- Departamento de Química, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Elaine M Souza-Fagundes
- Departamento de Química, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Heloisa Beraldo
- Departamento de Química, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, Minas Gerais, Brazil
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