Structures of topoisomerase V in complex with DNA reveal unusual DNA-binding mode and novel relaxati

Osterman, Amy; Mondragon, Alfonso

doi:10.7554/eLife.72702

Structures of topoisomerase V in complex with DNA reveal unusual DNA-binding mode and novel relaxati

Journal Article · 01 August 2022 · eLIFE J.

DOI:https://doi.org/10.7554/eLife.72702· OSTI ID:1901145

Osterman, Amy; Mondragon, Alfonso

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; NCI; NIGMS

OSTI ID:: 1901145

Journal Information:: eLIFE J., Journal Name: eLIFE J. Vol. 11

Country of Publication:: United States

Language:: ENGLISH

References (54)

Nonlinear partial differential equations and applications: The mechanism of topoisomerase I poisoning by a camptothecin analog Staker, B. L.; Hjerrild, K.; Feese, M. D. Proceedings of the National Academy of Sciences, Vol. 99, Issue 24 https://doi.org/10.1073/pnas.242259599	journal	November 2002
Structure and mechanism of nucleases regulated by SLX4 Nowotny, Marcin; Gaur, Vineet Current Opinion in Structural Biology, Vol. 36 https://doi.org/10.1016/j.sbi.2016.01.003	journal	February 2016
Origin and evolution of DNA topoisomerases Forterre, Patrick; Gribaldo, Simonetta; Gadelle, Danièle Biochimie, Vol. 89, Issue 4 https://doi.org/10.1016/j.biochi.2006.12.009	journal	April 2007
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Data processing and analysis with the autoPROC toolbox Vonrhein, Clemens; Flensburg, Claus; Keller, Peter Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911007773	journal	March 2011
A type IB topoisomerase with DNA repair activities Belova, G. I.; Prasad, R.; Kozyavkin, S. A. Proceedings of the National Academy of Sciences, Vol. 98, Issue 11 https://doi.org/10.1073/pnas.111040498	journal	May 2001
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Biochemical Characterization of the Topoisomerase Domain of Methanopyrus kandleri Topoisomerase V Rajan, Rakhi; Osterman, Amy K.; Gast, Alexandra T. Journal of Biological Chemistry, Vol. 289, Issue 42 https://doi.org/10.1074/jbc.M114.590711	journal	August 2014
Structural Basis for Specificity in the Poxvirus Topoisomerase Perry, Kay; Hwang, Young; Bushman, Frederic D. Molecular Cell, Vol. 23, Issue 3 https://doi.org/10.1016/j.molcel.2006.06.015	journal	August 2006
Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography Foadi, James; Aller, Pierre; Alguel, Yilmaz Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 8 https://doi.org/10.1107/S0907444913012274	journal	July 2013
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes Davis, I. W.; Murray, L. W.; Richardson, J. S. Nucleic Acids Research, Vol. 32, Issue Web Server https://doi.org/10.1093/nar/gkh398	journal	July 2004
DNA Topoisomerases Maxwell, Anthony; Bush, Natassja G.; Evans-Roberts, Katherine EcoSal Plus, Vol. 6, Issue 2 https://doi.org/10.1128/ecosalplus.ESP-0010-2014	journal	October 2015
Identification of one of the apurinic/apyrimidinic lyase active sites of topoisomerase V by structural and functional studies Rajan, Rakhi; Prasad, Rajendra; Taneja, Bhupesh Nucleic Acids Research, Vol. 41, Issue 1 https://doi.org/10.1093/nar/gks1017	journal	November 2012
Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB Koster, Daniel A.; Croquette, Vincent; Dekker, Cees Nature, Vol. 434, Issue 7033 https://doi.org/10.1038/nature03395	journal	March 2005
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Common fold in helix-hairpin-helix proteins Shao, X. Nucleic Acids Research, Vol. 28, Issue 14 https://doi.org/10.1093/nar/28.14.2643	journal	July 2000
Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases Taneja, Bhupesh; Patel, Asmita; Slesarev, Alexei The EMBO Journal, Vol. 25, Issue 2 https://doi.org/10.1038/sj.emboj.7600922	journal	January 2006
Structures of Minimal Catalytic Fragments of Topoisomerase V Reveals Conformational Changes Relevant for DNA Binding Rajan, Rakhi; Taneja, Bhupesh; Mondragón, Alfonso Structure, Vol. 18, Issue 7 https://doi.org/10.1016/j.str.2010.03.006	journal	July 2010
Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A Pavletich, N.; Pabo, C. Science, Vol. 252, Issue 5007 https://doi.org/10.1126/science.2028256	journal	May 1991
Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I Lima, Christopher D.; Wang, James C.; Mondragón, Alfonso Nature, Vol. 367, Issue 6459 https://doi.org/10.1038/367138a0	journal	January 1994
DNA topoisomerase V: a new fold of mysterious origin Forterre, Patrick Trends in Biotechnology, Vol. 24, Issue 6 https://doi.org/10.1016/j.tibtech.2006.04.006	journal	June 2006
Automated Structure Solution With autoSHARP Vonrhein, Clemens; Blanc, Eric; Roversi, Pietro Macromolecular Crystallography Protocols, Volume 2 https://doi.org/10.1385/1-59745-266-1:215	book	January 2006
Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion Moreno-Herrero, F. Nucleic Acids Research, Vol. 33, Issue 18 https://doi.org/10.1093/nar/gki906	journal	October 2005
The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target Mak, A. N. -S.; Bradley, P.; Cernadas, R. A. Science, Vol. 335, Issue 6069 https://doi.org/10.1126/science.1216211	journal	January 2012
Intramolecular synapsis of duplex DNA by vaccinia topoisomerase Shuman, S. The EMBO Journal, Vol. 16, Issue 21 https://doi.org/10.1093/emboj/16.21.6584	journal	November 1997
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
Replication Clamps and Clamp Loaders Hedglin, M.; Kumar, R.; Benkovic, S. J. Cold Spring Harbor Perspectives in Biology, Vol. 5, Issue 4 https://doi.org/10.1101/cshperspect.a010165	journal	April 2013
Structure, Molecular Mechanisms, and Evolutionary Relationships in DNA Topoisomerases Corbett, Kevin D.; Berger, James M. Annual Review of Biophysics and Biomolecular Structure, Vol. 33, Issue 1 https://doi.org/10.1146/annurev.biophys.33.110502.140357	journal	June 2004
DNA Topoisomerases and Their Poisoning by Anticancer and Antibacterial Drugs Pommier, Yves; Leo, Elisabetta; Zhang, HongLiang Chemistry & Biology, Vol. 17, Issue 5 https://doi.org/10.1016/j.chembiol.2010.04.012	journal	May 2010
A Bayesian approach to high-resolution X-ray crystallography: accurate density studies with program BUSTER Roversi, P.; Irwin, J.; Bricogne, G. Acta Crystallographica Section A Foundations of Crystallography, Vol. 52, Issue a1 https://doi.org/10.1107/S0108767396085790	journal	August 1996
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site Patel, Asmita; Yakovleva, Lyudmila; Shuman, Stewart Structure, Vol. 18, Issue 6 https://doi.org/10.1016/j.str.2010.03.007	journal	June 2010
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
The Domain Organization and Properties of Individual Domains of DNA Topoisomerase V, a Type 1B Topoisomerase with DNA Repair Activities Belova, Galina I.; Prasad, Rajendra; Nazimov, Igor V. Journal of Biological Chemistry, Vol. 277, Issue 7 https://doi.org/10.1074/jbc.M110131200	journal	December 2001
Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers. Zechiedrich, E. L.; Osheroff, N. The EMBO Journal, Vol. 9, Issue 13 https://doi.org/10.1002/j.1460-2075.1990.tb07908.x	journal	December 1990
An RNA topoisomerase. Wang, H.; Di Gate, R. J.; Seeman, N. C. Proceedings of the National Academy of Sciences, Vol. 93, Issue 18 https://doi.org/10.1073/pnas.93.18.9477	journal	September 1996
RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals Ahmad, Muzammil; Xue, Yutong; Lee, Seung Kyu Nucleic Acids Research, Vol. 44, Issue 13 https://doi.org/10.1093/nar/gkw508	journal	June 2016
Cellular roles of DNA topoisomerases: a molecular perspective Wang, James C. Nature Reviews Molecular Cell Biology, Vol. 3, Issue 6 https://doi.org/10.1038/nrm831	journal	June 2002
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Methanopyrus kandleritopoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso Nucleic Acids Research, Vol. 44, Issue 7 https://doi.org/10.1093/nar/gkw122	journal	February 2016
Purification and characterization of DNA topoisomerase V. An enzyme from the hyperthermophilic prokaryote Methanopyrus kandleri that resembles eukaryotic topoisomerase I. Slesarev, A. I.; Lake, J. A.; Stetter, K. O. Journal of Biological Chemistry, Vol. 269, Issue 5 https://doi.org/10.1016/S0021-9258(17)41862-X	journal	February 1994
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Crystal Structure of a Five-Finger GLI-DNA Complex: New Perspectives on Zinc Fingers Pavletich, Nikola P.; Pabo, Carl O. Science, Vol. 261, Issue 5129 https://doi.org/10.1126/science.8378770	journal	September 1993
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants Kabsch, W. Journal of Applied Crystallography, Vol. 26, Issue 6 https://doi.org/10.1107/S0021889893005588	journal	December 1993
Crystal Structures of Human Topoisomerase I in Covalent and Noncovalent Complexes with DNA Redinbo, M. R. Science, Vol. 279, Issue 5356 https://doi.org/10.1126/science.279.5356.1504	journal	March 1998
HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties Fleming, Patrick J.; Fleming, Karen G. Biophysical Journal, Vol. 114, Issue 4 https://doi.org/10.1016/j.bpj.2018.01.002	journal	February 2018
Electrostatics of nanosystems: Application to microtubules and the ribosome Baker, N. A.; Sept, D.; Joseph, S. Proceedings of the National Academy of Sciences, Vol. 98, Issue 18, p. 10037-10041 https://doi.org/10.1073/pnas.181342398	journal	August 2001
Helix–hairpin–helix motifs confer salt resistance and processivity on chimeric DNA polymerases Pavlov, Andrey R.; Belova, Galina I.; Kozyavkin, Sergei A. Proceedings of the National Academy of Sciences, Vol. 99, Issue 21 https://doi.org/10.1073/pnas.202127199	journal	October 2002
The helix-hairpin-helix DNA-binding motif: a structural basis for non- sequence-specific recognition of DNA Doherty, A. Nucleic Acids Research, Vol. 24, Issue 13 https://doi.org/10.1093/nar/24.13.2488	journal	July 1996
Preferential binding of human topoisomerase I to superhelical DNA. Madden, K. R.; Stewart, L.; Champoux, J. J. The EMBO Journal, Vol. 14, Issue 21 https://doi.org/10.1002/j.1460-2075.1995.tb00224.x	journal	November 1995
Roles of eukaryotic topoisomerases in transcription, replication and genomic stability Pommier, Yves; Sun, Yilun; Huang, Shar-yin N. Nature Reviews Molecular Cell Biology, Vol. 17, Issue 11 https://doi.org/10.1038/nrm.2016.111	journal	September 2016
DNA topoisomerase V is a relative of eukaryotic topoisomerase I from a hyperthermophilic prokaryote Slesarev, Alexe I.; Stetter, Karl O.; Lake, James A. Nature, Vol. 364, Issue 6439 https://doi.org/10.1038/364735a0	journal	August 1993
Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism Taneja, B.; Schnurr, B.; Slesarev, A. Proceedings of the National Academy of Sciences, Vol. 104, Issue 37 https://doi.org/10.1073/pnas.0701989104	journal	September 2007

Similar Records

Structures of topoisomerase V in complex with DNA reveal unusual DNA-binding mode and novel relaxa

Journal Article · 2022 · eLIFE J. · OSTI ID:1901099

Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site

Journal Article · 2010 · Structure · OSTI ID:1002532

Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate

Journal Article · 2010 · J. Mol. Biol. · OSTI ID:1007670

Structures of topoisomerase V in complex with DNA reveal unusual DNA-binding mode and novel relaxati

Citation Formats

References (54)

Similar Records

Related Subjects