1. Topoisomerase I (TOP1) dynamics: conformational transition from open to closed states
- Author
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Diane T. Takahashi, Danièle Gadelle, Keli Agama, Evgeny Kiselev, Hongliang Zhang, Emilie Yab, Stephanie Petrella, Patrick Forterre, Yves Pommier, Claudine Mayer, Biotechnologie et signalisation cellulaire (BSC), Université de Strasbourg (UNISTRA)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS)-Centre National de la Recherche Scientifique (CNRS), Microbiologie structurale - Structural Microbiology (Microb. Struc. (UMR_3528 / U-Pasteur_5)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Center for Cancer Research, National Cancer Institute [Bethesda] (NCI-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Université Paris Diderot - Paris 7 (UPD7), These studies have been supported by a European Research Council (ERC) Grant from the European Union’s Seventh Framework Program (FP/2007-2013) (Project EVOMOBIL-ERC) [340440 to P.F.], l′Agence Nationale de la Recherche [Project ESSPOIR ANR-17-CE12-0032 to T.T., D.G., S.P., and C.M.]. Grants from the Institut Pasteur (Paris), the CNRS (France), and the Université de Paris (France). The studies have also been supported by the Center for Cancer Research, the Intramural Program of the National Cancer Institute, National Institutes of Health [Z01-BC-006161 to K.A., E.K., H.Z., and Y.P.], We are grateful to the core facilities of the Institut Pasteur C2RT, and in particular the scientist from the Crystallography Platform: Ahmed Haouz, Patrick Weber, and Cedric Pissis for performing robot-driven crystallization trials and helpful discussions. We also wish to thank Ariel Mechaly for helping with phasing the SeMet TOP1 structure, and also acknowledge the staff of ESRF and SOLEIL Synchrotrons for assistance and support using beamlines ID29 (Grenoble, France) and SWING and PX2 (Saclay, France)., ANR-17-CE12-0032,ESSPOIR,Comprendre la structure de SPO11, ses fonctions et ses interactions(2017), and European Project: 340440,EC:FP7:ERC,ERC-2013-ADG,EVOMOBIL(2014)
- Subjects
Models, Molecular ,Multidisciplinary ,DNA Repair ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Protein Conformation ,Science ,DNA damage and repair ,General Physics and Astronomy ,DNA ,General Chemistry ,Sciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire ,Crystallography, X-Ray ,Article ,General Biochemistry, Genetics and Molecular Biology ,DNA-Binding Proteins ,DNA Topoisomerases, Type I ,Catalytic Domain ,Humans ,Camptothecin ,Structural biology ,Sequence Alignment ,DNA Damage ,X-ray crystallography - 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.
- Published
- 2022