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DNA topoisomerases: harnessing and constraining energy to govern chromosome topology

Published online by Cambridge University Press:  29 August 2008

Allyn J. Schoeffler  and
James M. Berger
Allyn J. Schoeffler
Affiliation:
Department of Molecular and Cell Biology, California Institute for Quantitative Biology, University of California-Berkeley, Berkeley, CA, USA
James M. Berger*
Affiliation:
Department of Molecular and Cell Biology, California Institute for Quantitative Biology, University of California-Berkeley, Berkeley, CA, USA
*
*Author for correspondence: Dr J. M. Berger, Department of Molecular and Cell Biology, California Institute for Quantitative Biology, University of California-Berkeley, Stanley Hall 3220, Berkeley, CA 94720-3220, USA.  Tel.: 510-643-9483; Fax: 510-666-2768; Email: [email protected]
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Abstract

DNA topoisomerases are a diverse set of essential enzymes responsible for maintaining chromosomes in an appropriate topological state. Although they vary considerably in structure and mechanism, the partnership between topoisomerases and DNA has engendered commonalities in how these enzymes engage nucleic acid substrates and control DNA strand manipulations. All topoisomerases can harness the free energy stored in supercoiled DNA to drive their reactions; some further use the energy of ATP to alter the topology of DNA away from an enzyme-free equilibrium ground state. In the cell, topoisomerases regulate DNA supercoiling and unlink tangled nucleic acid strands to actively maintain chromosomes in a topological state commensurate with particular replicative and transcriptional needs. To carry out these reactions, topoisomerases rely on dynamic macromolecular contacts that alternate between associated and dissociated states throughout the catalytic cycle. In this review, we describe how structural and biochemical studies have furthered our understanding of DNA topoisomerases, with an emphasis on how these complex molecular machines use interfacial interactions to harness and constrain the energy required to manage DNA topology.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 41 , Issue 1 , February 2008 , pp. 41 - 101
Copyright
Copyright © 2008 Cambridge University Press

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References

Aburashidova, G., Radulescu, S., Sandoval, O., Zahariev, S., Danailov, M. B., Demidovich, A., Santamaria, L., Biamonti, G., Riva, S. & Falaschi, A. (2007). Functional interactions of DNA topoisomerases with a human replication origin. EMBO Journal 26, 998–1009.CrossRefGoogle Scholar
Adams, D. E., Shekhtman, E. M., Zechiedrich, E. L., Schmid, M. B. & Cozzarelli, N. R. (1992). The role of topoisomerase IV in partitioning bacterial replicons and the structure of catenated intermediates in DNA replication. Cell 71, 277–288.CrossRefGoogle ScholarPubMed
Adrian, M., ten Heggeler-Bordier, B., Wahli, W., Stasiak, A. Z., Stasiak, A. & Dubochet, J. (1990). Direct visualization of supercoiled DNA molecules in solution. EMBO Journal 9, 4551–4554.CrossRefGoogle ScholarPubMed
Ali, J. A., Jackson, A. P., Howells, A. J. & Maxwell, A. (1993). The 43-kilodalton N-terminal fragment of the DNA gyrase B protein hydrolyzes ATP and binds coumarin drugs. Biochemistry 32, 2717–2724.CrossRefGoogle ScholarPubMed
Ali, J. A., Orphanides, G. & Maxwell, A. (1995). Nucleotide binding to the 43-kilodalton N-terminal fragment of the DNA gyrase B protein. Biochemistry 34, 9801–9808.CrossRefGoogle Scholar
Andoh, T. & Ishida, R. (1998). Catalytic inhibitors of DNA topoisomerase II. Biochimica et Biophysica Acta 1400, 155–171.CrossRefGoogle ScholarPubMed
Aravind, L., Leipe, D. D. & Koonin, E. V. (1998). Toprim – a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Research 26, 4205–4213.CrossRefGoogle ScholarPubMed
Atomi, H., Matsumi, R. & Imanaka, T. (2004). Reverse gyrase is not a prerequisite for hyperthermophilic life. Journal of Bacteriology 186, 4829–4833.CrossRefGoogle Scholar
Bahng, S., Mossessova, E., Nurse, P. & Marians, K. J. (2000). Mutational analysis of Escherichia coli topoisomerase IV: III. Identification of a region of parE involved in covalent catalysis. Journal of Biological Chemistry 275, 4112–4117.CrossRefGoogle ScholarPubMed
Baird, C. L., Harkins, T. T., Morris, S. K. & Lindsley, J. E. (1999). Topoisomerase II drives DNA transport by hydrolyzing one ATP. Proceedings of the National Academy of Sciences USA 96, 13685–13690.CrossRefGoogle ScholarPubMed
Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. (2001). Electrostatics of nanosystems: application to microtubules and the ribosome. Proceedings of the National Academy of Sciences USA 98, 10037–10041.CrossRefGoogle ScholarPubMed
Baldi, M. I., Benedetti, P., Mattoccia, E. & Toccini-Valentini, G. P. (1980). In vitro catenation and decatenation of DNA and a novel eukaryotic ATP dependent topoisomerase. Cell 20, 461–467.CrossRefGoogle Scholar
Bates, A. D. & Maxwell, A. (2005). DNA Topology, 2nd edn. Oxford: Oxford University Press.CrossRefGoogle Scholar
Bates, A. D. & Maxwell, A. (2007). Energy coupling in type II topoisomerases: why do they hydrolyze ATP? Biochemistry 46, 7929–7941.CrossRefGoogle ScholarPubMed
Bauman, M. E., Holden, J. A., Brown, K. A., Harker, W. G. & Perkins, S. L. (1997). Differential immunohistochemical staining for DNA topoisomerase II alpha and beta in human tissues and for DNA topoisomerase II beta in non-Hodgkin's lymphomas. Modern Pathology 10, 168–175.Google ScholarPubMed
Bellon, S., Parsons, J. D., Wei, Y., Hayakawa, K., Swenson, L. L., Charifson, P. S., Lippke, J. A., Aldape, R. & Gross, C. H. (2004). Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potentcy against topoisomerase IV and DNA gyrase. Antimicrobial Agents and Chemotherapy 48, 1856–1864.CrossRefGoogle Scholar
Belova, G. I., Prasad, R., Kozyavkin, S. A., Lake, J. A., Wilson, S. H. & Slesarev, A. I. (2001). A type IB topoisomerase with DNA repair activities. Proceedings of the National Academy of Sciences USA 98, 6015–6020.CrossRefGoogle ScholarPubMed
Benarroch, D., Claverie, J. M., Raoult, D. & Shuman, S. (2006). Characterization of mimivirus DNA topoisomerase IB suggests horizontal gene transfer between eukaryal viruses and bacteria. Journal of Virology 80, 314–321.CrossRefGoogle ScholarPubMed
Berger, J. M., Gamblin, S. J., Harrison, S. C. & Wang, J. C. (1996). Structure and mechanism of DNA topoisomerase II. Nature 379, 225–232.CrossRefGoogle ScholarPubMed
Bergerat, A., De Massy, B., Gadelle, D., Varoutas, P. C., Nicolas, A. & Forterre, P. (1997). An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature 386, 414–417.CrossRefGoogle ScholarPubMed
Bergerat, A., Gadelle, D. & Forterre, P. (1994). Purification of a DNA topoisomerase II from the hyperthermophilic archaeon Sulfolobus shibatae. A thermostable enzyme with both bacterial and eucaryal features. Journal of Biological Chemistry 269, 27663–27669.CrossRefGoogle ScholarPubMed
Bjergbaek, L., Jensen, S., Westergaard, O. & Andersen, A. H. (1999). Using a biochemical approach to identify the primary dimerization regions in human DNA topoisomerase IIalpha. Journal of Biological Chemistry 274, 26529–26536.CrossRefGoogle ScholarPubMed
Bjergbaek, L., Kingma, P., Nielsen, I. S., Wang, Y., Westergaard, O., Osheroff, N. & Andersen, A. H. (2000). Communication between the ATPase and cleavage/religation domains of human topoisomerase IIalpha. Journal of Biological Chemistry 275, 13041–13048.CrossRefGoogle ScholarPubMed
Boles, T. C., White, J. H. & Cozzarelli, N. R. (1990). Structure of plectonemically supercoiled DNA. Journal of Molecular Biology 213, 931–951.CrossRefGoogle ScholarPubMed
Bouthier, De La Tour C., Portemer, C., Huber, R., Forterre, P. & Duguet, M. (1991). Reverse gyrase in thermophilic eubacteria. Journal of Bacteriology 173, 3921–3923.CrossRefGoogle Scholar
Bouthier, De La Tour C., Portemer, C., Nadal, M., Stetter, K. O., Forterre, P. & Duguet, M. (1990). Reverse gyrase, a hallmark of the hyperthermophilic archaebacteria. Journal of Bacteriology 172, 6803–6808.CrossRefGoogle Scholar
Breuer, C., Stacey, N. J., West, C. E., Zhao, Y., Chory, J., Tsukaya, H., Azumi, Y., Maxwell, A., Roberts, K. & Sugimoto-Shirasu, K. (2007). BIN4, a novel component of the plant DNA topoisomerase VI complex, is required for endoreplication in Arabidopsis. The Plant Cell 19, 3655–3668.CrossRefGoogle ScholarPubMed
Brino, L., Urzhumtsev, A., Mousli, M., Bronner, C., Mitschler, A., Oudet, P. & Moras, D. (2000). Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center. Journal of Biological Chemistry 275, 9468–9475.CrossRefGoogle ScholarPubMed
Brochier-Armanet, C. & Forterre, P. (2007). Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2, 83–93.CrossRefGoogle ScholarPubMed
Brown, P. O. & Cozzarelli, N. R. (1979). A sign inversion mechanism for enzymatic supercoiling of DNA. Science 206, 1081–1083.CrossRefGoogle ScholarPubMed
Brown, P. O. & Cozzarelli, N. R. (1981). Catenation and knotting of duplex DNA by type I topoisomerases: a mechanistic parallel with type 2 topoisomerases. Proceedings of the National Academy of Sciences USA 78, 843–847.CrossRefGoogle ScholarPubMed
Brown, P. O., Peebles, C. L. & Cozzarelli, N. R. (1979). A topoisomerase from Escherichia coli related to DNA gyrase. Proceedings of the National Academy of Sciences USA 76, 6110–6114.CrossRefGoogle ScholarPubMed
Buck, G. R. & Zechiedrich, E. L. (2004). DNA disentangling by type-2 topoisomerases. Journal of Molecular Biology 340, 933–939.CrossRefGoogle ScholarPubMed
Buhler, C., Lebbink, J. H., Bocs, C., Ladenstein, R. & Forterre, P. (2001). DNA topoisomerase VI generates ATP-dependent double-strand breaks with two-nucleotide overhangs. Journal of Biological Chemistry 276, 37215–37222.CrossRefGoogle ScholarPubMed
Burden, D. A. & Osheroff, N. (1998). Mechanism of action of eukaryotic topoisomerase II and drugs targeted to the enzyme. Biochimica et Biophysica Acta 1400, 139–154.CrossRefGoogle ScholarPubMed
Burnier, Y., Weber, C., Flammini, A. & Stasiak, A. (2007). Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases. Nucleic Acids Research 35, 5223–5231.CrossRefGoogle ScholarPubMed
Cairns, J. (1963). The bacterial chromosome and its manner of replication as seen by autoradiography. Journal of Molecular Biology 6, 208–213.CrossRefGoogle ScholarPubMed
Carey, J. F., Schultz, S. J., Sisson, L., Fazzio, T. G. & Champoux, J. J. (2003). DNA relaxation by human topoisomerase I occurs in the closed clamp conformation of the protein. Proceedings of the National Academy of Sciences USA 100, 5640–5645.CrossRefGoogle ScholarPubMed
Caron, P. R., Watt, P. & Wang, J. C. (1994). The C-terminal domain of Saccharomyces cerevisiae DNA topoisomerase II. Molecular and Cellular Biology 14, 3197–3207.Google ScholarPubMed
Carpenter, A. J. & Porter, A. C. (2004). Construction, characterization, and complementation of a conditional-lethal DNA topoisomerase IIalpha mutant human cell line. Molecular Biology of the Cell 15, 5700–5711.CrossRefGoogle ScholarPubMed
Champoux, J. J. (1981). DNA is linked to the rat liver nicking-closing enzyme by a phosphodiester bond to tyrosine. Journal of Biological Chemistry 256, 4805–4809.CrossRefGoogle Scholar
Champoux, J. J. (2001). DNA topoisomerases: structure, function, and mechanism. Annual Review of Biochemistry 70, 369–413.CrossRefGoogle ScholarPubMed
Chang, S., Hu, T. & Hsieh, T. S. (1998). Analysis of a core domain in Drosophila DNA topoisomerase II. Targeting of an antitumor agent ICRF-159. Journal of Biological Chemistry 273, 19822–19828.CrossRefGoogle ScholarPubMed
Changela, A., Digate, R. J. & Mondragon, A. (2001). Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Nature 411, 1077–1081.CrossRefGoogle ScholarPubMed
Changela, A., Digate, R. J. & Mondragon, A. (2007). Structural studies of E. coli topoisomerase–IIIDNA complexes reveal a novel type IA topoisomerase–DNA conformational intermediate. Journal of Molecular Biology 368, 105–118.CrossRefGoogle ScholarPubMed
Charvin, G., Strick, T. R., Bensimon, D. & Croquette, V. (2005a). Topoisomerase IV bends and overtwists DNA upon binding. Biophysics Journal 89, 384–392.CrossRefGoogle ScholarPubMed
Charvin, G., Strick, T. R., Bensimon, D. & Croquette, V. (2005b). Tracking topoisomerase activity at the single-molecule level. Annual Review of Biophysics and Biomolecular Structure 34, 201–219.CrossRefGoogle ScholarPubMed
Chen, S. J. & Wang, J. C. (1998). Identification of active site residues in Escherichia coli DNA topoisomerase I. Journal of Biological Chemistry 273, 6050–6056.CrossRefGoogle ScholarPubMed
Cheng, C., Kussie, P., Pavletich, N. & Shuman, S. (1998). Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. Cell 92, 841–850.CrossRefGoogle ScholarPubMed
Chillemi, G., Bruselles, A., Fiorani, P., Bueno, S. & Desideri, A. (2007). The open state of human topoisomerase I as probed by molecular dynamics simulation. Nucleic Acids Research 35, 3032–3038.CrossRefGoogle ScholarPubMed
Chillemi, G., Fiorani, P., Castelli, S., Bruselles, A., Benedetti, P. & Desideri, A. (2005). Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study. Nucleic Acids Research 33, 3339–3350.CrossRefGoogle ScholarPubMed
Chillemi, G., Redinbo, M., Bruselles, A. & Desideri, A. (2004). Role of the linker domain and the 203–214 N-terminal residues in the human topoisomerase I DNA complex dynamics. Biophysics Journal 87, 4087–4097.CrossRefGoogle ScholarPubMed
Chrencik, J. E., Staker, B. L., Burgin, A. B., Pourquier, P., Pommier, Y., Stewart, L. & Redinbo, M. R. (2004). Mechanisms of camptothecin resistance by human topoisomerase I mutations. Journal of Molecular Biology 339, 773–784.CrossRefGoogle ScholarPubMed
Classen, S., Olland, S. & Berger, J. M. (2003). Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187. Proceedings of the National Academy of Sciences USA 100, 10629–10634.CrossRefGoogle ScholarPubMed
Corbett, A. H., Zechiedrich, E. L. & Osheroff, N. (1992). A role for the passage helix in the DNA cleavage reaction of eukaryotic topoisomerase II: a two-site model for enzyme-mediated DNA cleavage. Journal of Biological Chemistry 267, 1188–1190.CrossRefGoogle ScholarPubMed
Corbett, K. D., Benedetti, P. & Berger, J. M. (2007). Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI. Nature Structural and Molecular Biology 14, 611–619.CrossRefGoogle ScholarPubMed
Corbett, K. D. & Berger, J. M. (2003a). Emerging roles for plant topoisomerase VI. Chemistry and Biology 10, 107–111.CrossRefGoogle ScholarPubMed
Corbett, K. D. & Berger, J. M. (2003b). Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution. EMBO Journal 22, 151–163.CrossRefGoogle ScholarPubMed
Corbett, K. D. & Berger, J. M. (2004). Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annual Review of Biophysics and Biomolecular Structure 33, 95–118.CrossRefGoogle ScholarPubMed
Corbett, K. D. & Berger, J. M. (2005). Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI. Structure 13, 873–882.CrossRefGoogle ScholarPubMed
Corbett, K. D., Schoeffler, A. J., Thomsen, N. D. & Berger, J. M. (2005). The structural basis for substrate specificity in DNA topoisomerase IV. Journal of Molecular Biology 351, 545–561.CrossRefGoogle ScholarPubMed
Corbett, K. D., Shultzaberger, R. K. & Berger, J. M. (2004). The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Proceedings of the National Academy of Sciences USA 101, 7293–7298.CrossRefGoogle ScholarPubMed
Costenaro, L., Grossmann, J. G., Ebel, C. & Maxwell, A. (2005). Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit. Structure 13, 287–296.CrossRefGoogle ScholarPubMed
Craig, N. L. & Nash, H. A. (1984). E. coli integration host factor binds to specific sites in DNA. Cell 39, 707–716.CrossRefGoogle ScholarPubMed
Crenshaw, D. G. & Hsieh, T. (1993). Function of the hydrophilic carboxyl terminus of type II DNA topoisomerase from Drosophila melanogaster. II. In vivo studies. Journal of Biological Chemistry 268, 21335–21343.CrossRefGoogle ScholarPubMed
Crick, F. H. (1976). Linking numbers and nucleosomes. Proceedings of the National Academy of Sciences USA 73, 2639–2643.CrossRefGoogle ScholarPubMed
Crisona, N. J., Strick, T. R., Bensimon, D., Croquette, V. & Cozzarelli, N. R. (2000). Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. Genes and Development 14, 2881–2892.CrossRefGoogle Scholar
Critchlow, S. E., O'Dea, M. H., Howells, A. J., Couturier, M., Gellert, M. & Maxwell, A. (1997). The interaction of the F plasmid killer protein, CcdB, with DNA gyrase: induction of DNA cleavage and blocking of transcription. Journal of Molecular Biology 273, 826–839.CrossRefGoogle Scholar
Crooks, G. E., Hon, G., Chandonia, J.-M. & Brenner, S. WebLogo. (2004). WebLogo: a sequence logo generator. Genome Research 14(6): 1188–1990.CrossRefGoogle ScholarPubMed
Dao-Thi, M. H., Van Melderen, L., De Genst, E., Afif, H., Buts, L., Wyns, L. & Loris, R. (2005). Molecular basis of gyrase poisoning by the addiction toxin CcdB. Journal of Molecular Biology 348, 1091–1102.CrossRefGoogle ScholarPubMed
Davies, D. R., Mushtaq, A., Interthal, H., Champoux, J. J. & Hol, W. G. (2006). The structure of the transition state of the heterodimeric topoisomerase I of Leishmania donovani as a vanadate complex with nicked DNA. Journal of Molecular Biology 357, 1202–1210.CrossRefGoogle ScholarPubMed
Declais, A. C., Marsault, J., Confalonieri, F., De La Tour, C. B. & Duguet, M. (2000). Reverse gyrase, the two domains intimately cooperate to promote positive supercoiling. Journal of Biological Chemistry 275, 19498–19504.CrossRefGoogle ScholarPubMed
Deibler, R. W., Mann, J. K., Sumners, D. W. L. & Zechiedrich, E. L. (2007). Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation. BMC Molecular Biology 8, 44–57.CrossRefGoogle ScholarPubMed
Dekker, N. H., Rybenkov, V. V., Duguet, M., Crisona, N. J., Cozzarelli, N. R., Bensimon, D. & Croquette, V. (2002). The mechanism of type IA topoisomerases. Proceedings of the National Academy of Sciences USA 99, 12126–12131.CrossRefGoogle ScholarPubMed
Delano, W. L. (2002). The PyMOL Molecular Graphics System. Palo Alto, CA: DeLano Scientific.Google Scholar
Depew, R. E., Liu, L. F. & Wang, J. C. (1978). Interaction between DNA and Escherichia coli protein omega. Formation of a complex between single-stranded DNA and omega protein. Journal of Biological Chemistry 253, 511–518.CrossRefGoogle ScholarPubMed
Depew, R. E. & Wang, J. C. (1975). Conformational fluctuations of DNA helix. Proceedings of the National Academy of Sciences USA, 72 4275–4279.CrossRefGoogle ScholarPubMed
Dereuddre, S., Delaporte, C. & Jacquemin-Sablon, A. (1997). Role of topoisomerase II beta in the resistance of 9-OH-ellipticine-resistant Chinese hamster fibroblasts to topoisomerase II inhibitors. Cancer Research 57, 4301–4308.Google ScholarPubMed
Dickey, J. S. & Osheroff, N. (2005). Impact of the C-terminal domain of topoisomerase II-alpha on the DNA cleavage activity of the human enzyme. Biochemistry 44, 11546–11554.CrossRefGoogle ScholarPubMed
Digate, R. J. & Marians, K. J. (1988). Identification of a potent decatenating enzyme from Escherichia coli. Journal of Biological Chemistry 263, 13366–13373.CrossRefGoogle ScholarPubMed
Domanico, P. L. & Tse-Dinh, Y. C. (1991). Mechanistic studies on E. coli DNA topoisomerase I: divalent ion effects. Journal of Inorganic Biochemistry 42, 87–96.CrossRefGoogle Scholar
Dong, K. C. & Berger, J. M. (2007). Structural basis for gate-DNA recognition and bending by type IIA topoisomerases. Nature 450, 1201–1205.CrossRefGoogle ScholarPubMed
Drake, F. H., Hofmann, G. A., Bartus, H. F., Mattern, M. R., Crooke, S. T. & Mirabelli, C. K. (1989). Biochemical and pharmacological properties of p170 and p180 forms of topoisomerase II. Biochemistry 28, 8154–8160.CrossRefGoogle ScholarPubMed
Drake, F. H., Zimmerman, J. P., McCabe, F. L., Bartus, H. F., Per, S. R., Sullivan, D. M., Ross, W. E., Mattern, M. R., Johnson, R. K. & Crooke, S. T. (1987). Purification of topoisomerase II from amsacrine-resistant P388 leukemia cells. Evidence for two forms of the enzyme. Journal of Biological Chemistry 262, 16739–16747.CrossRefGoogle ScholarPubMed
Drlica, K. (1992). Control of bacterial DNA supercoiling. Molecular Microbiology 6, 425–433.CrossRefGoogle ScholarPubMed
Drlica, K. & Zhao, X. (1997). DNA gyrase, topoisomerase IV, and the 4-quinolones. Microbiology and Molecular Biology Reviews 61, 377–392.Google ScholarPubMed
Duguet, M., Serre, M. C. & Bouthier De La Tour, C. (2006). A universal type IA topoisomerase fold. Journal of Molecular Biology 359, 805–812.CrossRefGoogle ScholarPubMed
Dutta, R. & Inouye, M. (2000). GHKL, an emergent ATPase/kinase superfamily. Trends in Biochemical Sciences 25, 24–28.CrossRefGoogle ScholarPubMed
Dynan, W. S., Jendrisak, J. J., Hager, D. A. & Burgess, R. R. (1981). Purification and characterization of wheat germ DNA topoisomerase I (nicking-closing enzyme). Journal of Biological Chemistry 256, 5860–5865.CrossRefGoogle ScholarPubMed
Espeli, O., Lee, C. & Marians, K. J. (2003). A physical and functional interaction between Escherichia coli FtsK and topoisomerase IV. Journal of Biological Chemistry 278, 44639–44644.CrossRefGoogle ScholarPubMed
Fass, D., Bogden, C. E. & Berger, J. M. (1999). Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands. Nature Structural Biology 6, 322–326.Google ScholarPubMed
Feinberg, H., Changela, A. & Mondragon, A. (1999a). Protein–nucleotide interactions in E. coli DNA topoisomerase I. Nature Structural Biology 6, 961–968.Google ScholarPubMed
Feinberg, H., Lima, C. D. & Mondragon, A. (1999b). Conformational changes in E. coli DNA topoisomerase I. Nature Structural Biology 6, 918–922.Google ScholarPubMed
Fiorani, P., Bruselles, A., Falconi, M., Chillemi, G., Desideri, A. & Benedetti, P. (2003). Single mutation in the linker domain confers protein flexibility and camptothecin resistance to human topoisomerase I. Journal of Biological Chemistry 278, 43268–43275.CrossRefGoogle ScholarPubMed
Forterre, P., Bergerat, A. & Lopez-Garcia, P. (1996). The unique DNA topology and DNA topoisomerases of hyperthermophilic archaea. FEMS Microbiology Reviews 18, 237–248.CrossRefGoogle ScholarPubMed
Forterre, P., Gribaldo, S., Gadelle, D. & Serre, M. C. (2007). Origin and evolution of DNA topoisomerases. Biochimie 89, 427–446.CrossRefGoogle ScholarPubMed
Frohlich, R. F., Andersen, F. F., Westergaard, O., Andersen, A. H. & Knudsen, B. R. (2004). Regions within the N-terminal domain of human topoisomerase I exert important functions during strand rotation and DNA binding. Journal of Molecular Biology 336, 93–103.CrossRefGoogle ScholarPubMed
Frohlich, R. F., Veigaard, C., Andersen, F. F., McClendon, A. K., Gentry, A. C., Andersen, A. H., Osheroff, N., Stevnsner, T. & Knudsen, B. R. (2007). Tryptophane-205 of human topoisomerase I is essential for camptothecin inhibition of negative but not positive supercoil removal. Nucleic Acids Research 35, 5170–6180.CrossRefGoogle Scholar
Gadelle, D., Filee, J., Buhler, C. & Forterre, P. (2003). Phylogenomics of type II DNA topoisomerases. BioEssays 25, 232–242.CrossRefGoogle ScholarPubMed
Gajiwala, K. S. & Burley, S. K. (2000). Winged helix proteins. Current Opinion in Structural Biology 10, 110–116.CrossRefGoogle ScholarPubMed
Gellert, M., Mizuuchi, K., O'Dea, M. H. & Nash, H. A. (1976). DNA gyrase: an enzyme that introduces superhelical turns in DNA. Proceedings of the National Academy of Sciences USA 73, 3872–3876.CrossRefGoogle Scholar
Gore, J., Bryant, Z., Stone, M. D., Nollmann, M., Cozzarelli, N. R. & Bustamante, C. (2006). Mechanochemical analysis of DNA gyrase using rotor bead tracking. Nature 439, 100–104.CrossRefGoogle ScholarPubMed
Gottler, T. & Klostermeier, D. (2007). Dissection of the nucleotide cycle of B. subtilis DNA gyrase and its modulation by DNA. Journal of Molecular Biology 367, 1392–1404.CrossRefGoogle ScholarPubMed
Graille, M., Cladiere, L., Durand, D., Lecointe, F., Gadelle, D., Quevillon-Cheruel, S., Vachette, P., Forterre, P. & van Tilbeurgh, H. (2008). Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms. Structure 16, 360–370.CrossRefGoogle ScholarPubMed
Grishin, N. V. (2000a). C-terminal domains of Escherichia coli topoisomerase I belong to the zinc-ribbon superfamily. Journal of Molecular Biology 299, 1165–1177.CrossRefGoogle Scholar
Grishin, N. V. (2000b). Two tricks in one bundle: helix–turn–helix gains enzymatic activity. Nucleic Acids Research 28, 2229–2233.CrossRefGoogle ScholarPubMed
Grue, P., Grasser, A., Sehested, M., Jensen, P. B., Uhse, A., STraub, T., Ness, W. & Boege, F. (1998). Essential mitotic functions of DNA topoisomerase IIalpha are not adopted by topoisomerase IIbeta in human H69 cells. Journal of Biological Chemistry 273, 33660–33666.CrossRefGoogle Scholar
Hanai, R. & Wang, J. C. (1994). Protein footprinting by the combined use of reversible and irreversible lysine modifications. Proceedings of the National Academy of Sciences USA 91, 11904–11908.CrossRefGoogle ScholarPubMed
Hansen, G., Harrenga, A., Wieland, B., Schomburg, D. & Reinemer, P. (2006). Crystal structure of full length topoisomerase I from Thermotoga maritima. Journal of Molecular Biology 358, 1328–1340.CrossRefGoogle ScholarPubMed
Har-Vardi, I., Mali, R., Breietman, M., Sonin, Y., Albotiano, S., Levitas, E., Potashnik, G. & Priel, E. (2007). DNA topoisomerases I and II in human mature sperm cells: characterization and unique properties. Human Reproduction 22, 2183–2189.CrossRefGoogle Scholar
Harkins, T. T., Lewis, T. J. & Lindsley, J. E. (1998). Pre-steady-state analysis of ATP hydrolysis by Saccharomyces cerevisiae DNA topoisomerase II. 2. Kinetic mechanism for the sequential hydrolysis of two ATP. Biochemistry 37, 7299–7312.CrossRefGoogle ScholarPubMed
Harkins, T. T. & Lindsley, J. E. (1998). Pre-steady-state analysis of ATP hydrolysis by Saccharomyces cerevisiae DNA topoisomerase II. 1. A DNA-dependent burst in ATP hydrolysis. Biochemistry 37, 7292–7298.CrossRefGoogle ScholarPubMed
Harmon, F. G., Digate, R. J. & Kowalczykowsji, S. C. (1999). RecQ helicase and topoisomerase III comprise a novel DNA strand passage function: a conserved mechanism for control of DNA recombination. Molecular Cell 3, 611–620.CrossRefGoogle ScholarPubMed
Harrison, S. C. & Aggarwal, A. K. (1990). DNA recognition by proteins with the helix–turn–helix motif. Annual Review of Biochemistry 59, 933–969.CrossRefGoogle ScholarPubMed
Hartung, F. & Puchta, H. (2001). Molecular characterization of homologues of both subunits A (SPO11) and B of the archaebacterial topoisomerase 6 in plants. Gene 271, 81–86.CrossRefGoogle Scholar
Heck, M. M. & Earnshaw, W. C. (1986). Topoisomerase II: a specific marker for cell proliferation. Journal of Cell Biology 103, 2569–2581.CrossRefGoogle ScholarPubMed
Heddle, J. G., Mitelheiser, S., Maxwell, A. & Thomson, N. H. (2004). Nucleotide binding to DNA gyrase causes loss of DNA wrap. Journal of Molecular Biology 337, 597–610.CrossRefGoogle ScholarPubMed
Hegde, S. S., Vetting, M. W., Roderick, S. L., Mitchenall, L. A., Maxwell, A., Takiff, H. E. & Blanchard, J. S. (2005). A fluoroquinolone resistance protein from Mycobacterium tuberculosis that mimics DNA. Science 308, 1480–1483.CrossRefGoogle ScholarPubMed
Hiasa, H., Digate, R. J. & Marians, K. J. (1994). Decatenating activity of Escherichia coli DNA gyrase and topoisomerases I and III during oriC and pBR322 DNA replication in vitro. Journal of Biological Chemistry 269, 2093–2099.CrossRefGoogle ScholarPubMed
Holmes, V. F. & Cozzarelli, N. R. (2000). Closing the ring: links between SMC proteins and chromosome partitioning, condensation, and supercoiling. Proceedings of the National Academy of Sciences USA 97, 1322–1324.CrossRefGoogle ScholarPubMed
Hooper, D. C. & Rubinstein, E. (2003). Quinolone Antimicrobial Agents, 3rd edn. Washington, DC: ASM Press.CrossRefGoogle Scholar
Howard, M. T., Lee, M. P., Hsieh, T. S. & Griffith, J. D. (1991). Drosophila topoisomerase II–DNA interactions are affected by DNA structure. Journal of Molecular Biology 217, 53–62.CrossRefGoogle ScholarPubMed
Hsiang, Y. H., Hertzberg, R., Hecht, S. M. & Liu, L. F. (1985). Camptothecin induces protein-linked DNA breaks va mammalian DNA topoisomerase I. Journal of Biological Chemistry 260, 14873–14878.CrossRefGoogle Scholar
Hsiang, Y. H., Wu, H. Y. & Liu, L. F. (1988). Proliferation-dependent regulation of DNA topoisomerase II in cultured human cells. Cancer Research 48, 3230–3235.Google ScholarPubMed
Hsieh, T. & Brutlag, D. (1980). ATP-dependent DNA topoisomerase from D. melanogaster reversibly catenates duplex DNA rings. Cell 21, 115–125.CrossRefGoogle Scholar
Hsieh, T. J., Farh, L., Huang, W. M. & Chan, N. L. (2004). Structure of the topoisomerase IV C-terminal domain: a broken beta-propeller implies a role as geometry facilitator in catalysis. Journal of Biological Chemistry 279, 55587–55593.CrossRefGoogle Scholar
Hsieh, T. S. & Capp, C. (2005). Nucleotide- and stoichiometry-dependent DNA supercoiling by reverse gyrase. Journal of Biological Chemistry 280, 20467–20475.CrossRefGoogle ScholarPubMed
Hsieh, T. S. & Plank, J. L. (2006). Reverse gyrase functions as a DNA renaturase: annealing of complementary single-stranded circles and positive supercoiling of a bubble substrate. Journal of Biological Chemistry 281, 5640–5647.CrossRefGoogle ScholarPubMed
Huang, W. M. (1996). Bacterial diversity based on type II DNA topoisomerase genes. Annual Review of Genetics, 30 79–107.CrossRefGoogle ScholarPubMed
Huang, Y. Y., Deng, J. Y., Gu, J., Zhang, Z. P., Maxwell, A., Bi, L. J., Chen, Y. Y., Zhou, Y. F., Yu, Z. N. & Zhang, X. E. (2006). The key DNA-binding residues in the C-terminal domain of Mycobacterium tuberculosis DNA gyrase A subunit (GyrA). Nucleic Acids Research 34, 5650–5659.CrossRefGoogle ScholarPubMed
Hwang, Y., Wang, B. & Bushman, F. D. (1998). Molluscum contagiosum virus topoisomerase: purification, activities, and response to inhibitors. Journal of Virology 72, 3401–3406.CrossRefGoogle ScholarPubMed
Interthal, H., Quigley, P. M., Hol, W. G. & Champoux, J. J. (2004). The role of lysine 532 in the catalytic mechanism of human topoisomerase I. Journal of Biological Chemistry 279, 2984–2992.CrossRefGoogle ScholarPubMed
Isaacs, R. J., Davies, S. L., Sandri, M. I., Redwood, C., Wells, N. J. & Hickson, I. D. (1998). Physiological regulation of eukaryotic topoisomerase II. Biochimica et Biophysica Acta 1400, 121–137.CrossRefGoogle ScholarPubMed
Iwabata, K., Koshiyama, A., Yamaguchi, T., Sugawara, H., Hamada, F. N., Namekawa, S. H., Ishii, S., Ishizaki, T., Chiku, H., Nara, T. & Sakaguchi, K. (2005). DNA topoisomerase II interacts with Lim15/Dmc1 in meiosis. Nucleic Acids Research 33, 5809–5818.CrossRefGoogle ScholarPubMed
Iyer, L. M., Leipe, D. D., Koonin, E. V. & Aravind, L. (2004). Evolutionary history and higher order classification of AAA+ ATPases. Journal of Structural Biology 146, 11–31.CrossRefGoogle ScholarPubMed
Jain, P. & Nagaraja, V. (2002). An orphan gyrB in the Mycobacterium smegmatis genome uncovered by comparative genomics. Journal of Genetics 81, 105–110.CrossRefGoogle ScholarPubMed
Jain, P. & Nagaraja, V. (2005). An atypical type II topoisomerase from Mycobacterium smegmatis with positive supercoiling activity. Molecular Microbiology 58, 1392–1405.CrossRefGoogle ScholarPubMed
Ju, B. G., Lunyak, V. V., Perissi, V., Garcia-Bassets, I., Rose, D. W., Glass, C. K. & Rosenfeld, M. G. (2006). A topoisomerase II beta-mediated dsDNA break required for regulated transcription. Science 312, 1798–1802.CrossRefGoogle Scholar
Jungblut, S. P. & Klostermeier, D. (2007). Adenosine 5′-O-(3-thio)triphosphate (ATPgammaS) promotes positive supercoiling of DNA by T. maritima reverse gyrase. Journal of Molecular Biology 371, 197–209.CrossRefGoogle ScholarPubMed
Kampmann, M. & Stock, D. (2004). Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling. Nucleic Acids Research 32, 3537–3545.CrossRefGoogle ScholarPubMed
Kampranis, S. C., Bates, A. D. & Maxwell, A. (1999). A model for the mechanism of strand passage by DNA gyrase. Proceedings of the National Academy of Sciences USA 96, 8414–8419.CrossRefGoogle Scholar
Kampranis, S. C. & Maxwell, A. (1996). Conversion of DNA gyrase into a conventional type II topoisomerase. Proceedings of the National Academy of Sciences USA 93, 14416–14421.CrossRefGoogle ScholarPubMed
Kato, J., Nishimura, Y., Imamura, R., Niki, H., Hiraga, S. & Suzuki, H. (1990). New topoisomerase essential for chromosome segregation in E. coli. Cell 63, 393–404.CrossRefGoogle ScholarPubMed
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30, 3059–3066.CrossRefGoogle ScholarPubMed
Keeney, S., Giroux, C. N. & Kleckner, N. (1997). Meiosis-specific DNA double-strand breaks are catalyzed by Spo11, a member of a widely conserved protein family. Cell 88, 375–384.CrossRefGoogle ScholarPubMed
Kikuchi, A. & Asai, K. (1984). Reverse gyrase – a topoisomerase which introduces positive superhelical turns into DNA. Nature 309, 677–681.CrossRefGoogle ScholarPubMed
Kim, R. A. & Wang, J. C. (1992). Identification of the yeast TOP3 gene product as a single strand-specific DNA topoisomerase. Journal of Biological Chemistry 267, 17178–17185.CrossRefGoogle ScholarPubMed
Kirkegaard, K. & Wang, J. C. (1985). Bacterial DNA topoisomerase I can relax positively supercoiled DNA containing a single-stranded loop. Journal of Molecular Biology 185, 625–637.CrossRefGoogle ScholarPubMed
Koster, D. A., Croquette, V., Dekker, C., Shuman, S. & Dekker, N. H. (2005). Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature 434, 671–674.CrossRefGoogle ScholarPubMed
Koster, D. A., Palle, K., Bot, E. S., Bjornsti, M. A. & Dekker, N. H. (2007). Antitumour drugs impede DNA uncoiling by topoisomerase I. Nature 448, 213–217.CrossRefGoogle ScholarPubMed
Kozyavkin, S. A., Pushkin, A. V., Eiserling, F. A., Stetter, K. O., Lake, J. A. & Slesarev, A. I. (1995). DNA enzymology above 100 degrees C. Topoisomerase V unlinks circular DNA at 80–122 degrees C. Journal of Biological Chemistry 270, 13593–13595.CrossRefGoogle ScholarPubMed
Kramlinger, V. M. & Hiasa, H. (2006). The ‘GyrA-box’ is required for the ability of DNA gyrase to wrap DNA and catalyze the supercoiling reaction. Journal of Biological Chemistry 281, 3738–3742.CrossRefGoogle ScholarPubMed
Krogh, B. O., Claeboe, C. D., Hecht, S. M. & Shuman, S. (2001). Effect of 2′–5′ phosphodiesters on DNA transesterification by vaccinia topoisomerase. Journal of Biological Chemistry 276, 20907–20912.CrossRefGoogle ScholarPubMed
Krogh, B. O. & Shuman, S. (2000). Catalytic mechanism of DNA topoisomerase IB. Molecular Cell 5, 1035–1041.CrossRefGoogle ScholarPubMed
Krogh, B. O. & Shuman, S. (2002a). A poxvirus-like type IB topoisomerase family in bacteria. Proceedings of the National Academy of Sciences USA 99, 1853–1858.CrossRefGoogle ScholarPubMed
Krogh, B. O. & Shuman, S. (2002b). Proton relay mechanism of general acid catalysis by DNA topoisomerase IB. Journal of Biological Chemistry 277, 5711–5714.CrossRefGoogle ScholarPubMed
Kurz, E. U., Leader, K. B., Kroll, D. J., Clark, M. & Gieseler, F. (2000). Modulation of human DNA topoisomerase IIalpha function by interaction with 14-3-3epsilon. Journal of Biological Chemistry 275, 13948–13954.CrossRefGoogle ScholarPubMed
Lamour, V., Hoermann, L., Jeltsch, J. M., Oudet, P. & Moras, D. (2002). An open conformation of the Thermus thermophilus gyrase B ATP-binding domain. Journal of Biological Chemistry 277, 18947–18953.CrossRefGoogle ScholarPubMed
Laponogov, I., Veselkov, D. A., Sohi, M. K., Pan, X., Achari, A., Yang, C., Ferrara, J. D., Fisher, L. M. & Sanderson, M. R. (2007). Breakage–reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target. PLoS One 2(3), e301.CrossRefGoogle ScholarPubMed
Lavrukhin, O. V., Fortune, J. M., Wood, T. G., Burbank, D. E., van Etten, J. L., Osheroff, N. & Lloyd, R. S. (2000). Topoisomerase II from Chlorella virus PBCV-1. Journal of Biological Chemistry 275, 6915–6921.CrossRefGoogle ScholarPubMed
Levine, C., Hiasa, H. & Marians, K. J. (1998). DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome replication, and drug sensitivities. Biochimica et Biophysica Acta 1400, 29–43.CrossRefGoogle ScholarPubMed
Li, Z., Hiasa, H. & Digate, R. (2006). Characterization of a unique type IA topoisomerase in Bacillus cereus. Molecular Microbiology 60, 140–151.CrossRefGoogle ScholarPubMed
Li, Z., Mondragon, A., Hiasa, H., Marians, K. J. & Digate, R. J. (2000). Identification of a unique domain essential for Escherichia coli DNA topoisomerase III-catalysed decatenation of replication intermediates. Molecular Microbiology 35, 888–895.CrossRefGoogle ScholarPubMed
Lima, C. D., Wang, J. C. & Mondragon, A. (1994). Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I. Nature 367, 138–146.CrossRefGoogle ScholarPubMed
Lindsley, J. E. & Wang, J. C. (1993). On the coupling between ATP usage and DNA transport by yeast DNA topoisomerase II. Journal of Biological Chemistry 268, 8096–8104.CrossRefGoogle ScholarPubMed
Linka, R. M., Porter, A. C., Volkov, A., Mielke, C., Boege, F. & Christensen, M. O. (2007). C-terminal regions of topoisomerase IIalpha and IIbeta determine isoform-specific functioning of the enzymes in vivo. Nucleic Acids Research 35, 3810–3822.CrossRefGoogle ScholarPubMed
Liu, L. F., Liu, C. C. & Alberts, B. M. (1979). T4 DNA topoisomerase: a new ATP-dependent enzyme essential for initiation of T4 bacteriophage DNA replication. Nature 281, 456–461.CrossRefGoogle ScholarPubMed
Liu, L. F., Rowe, T. C., Yang, L., Tewey, K. M. & Chen, G. L. (1983). Cleavage of DNA by mammalian DNA topoisomerase II. Journal of Biological Chemistry 258, 15365–15370.CrossRefGoogle ScholarPubMed
Liu, L. F. & Wang, J. C. (1978). DNA–DNA gyrase complex: the wrapping of the DNA duplex outside the enzyme. Cell 15, 979–984.CrossRefGoogle ScholarPubMed
Liu, L. F. & Wang, J. C. (1979). Interaction between DNA and Escherichia coli DNA topoisomerase: I. Formation of complexes between the protein and superhelical and nonsuperhelical duplex DNAs. Journal of Biological Chemistry 254, 11082–11088.CrossRefGoogle ScholarPubMed
Liu, L. F. & Wang, J. C. (1987). Supercoiling of the DNA template during transcription. Proceedings of the National Academy of Sciences USA 84, 7024–7027.CrossRefGoogle ScholarPubMed
Lopez, C. R., Yang, S., Deibler, R. W., Ray, S. A., Pennington, J. M., Digate, R. J., Hastings, P. J., Rosenberg, S. M. & Zechiedrich, E. L. (2005). A role for topoisomerase III in a recombination pathway alternative to RuvABC. Molecular Microbiology 58, 80–101.CrossRefGoogle Scholar
Lou, Z., Minter-Dykhouse, K. & Chen, J. (2005). BRCA1 participates in DNA decatenation. Nature Structural and Molecular Biology 12, 589–593.CrossRefGoogle ScholarPubMed
Malik, S. B., Ramesh, M. A., Hulstrand, A. M. & Logsdon, J. M. J. (2007). Protist homologs of the meiotic Spo11 gene and topoisomerase VI reveal and evolutionary history of gene duplication and lineage-specific loss. Molecular Biology and Evolution 24, 2827–2841.CrossRefGoogle ScholarPubMed
Mao, Y., Desai, S. D. & Liu, L. F. (2000). SUMO-1 conjugation to human DNA topoisomerase II isoenzymes. Journal of Biological Chemistry 275, 26066–26073.CrossRefGoogle Scholar
Maxwell, A., Costenaro, L., Mitelheiser, S. & Bates, A. D. (2005). Coupling ATP hydrolysis to DNA strand passage in type IIA DNA topoisomerases. Biochemical Society Transactions, 33, 1460–1464.CrossRefGoogle ScholarPubMed
Maxwell, A. & Lawson, D. M. (2003). The ATP-binding site of type II topoisomerases as a target for antibacterial drugs. Current Topics in Medicinal Chemistry 3, 283–303.CrossRefGoogle ScholarPubMed
McClendon, A. K., Dickey, J. S. & Osheroff, N. (2006). Ability of viral topoisomerase II to discern the handedness of supercoiled DNA: bimodal recognition of DNA geometry by type II enzymes. Biochemistry 45, 11674–11680.CrossRefGoogle ScholarPubMed
McClendon, A. K. & Osheroff, N. (2006). The geometry of DNA supercoils modulates topoisomerase-mediated DNA cleavage and enzyme response to anticancer drugs. Biochemistry 45, 3040–3050.CrossRefGoogle ScholarPubMed
McClendon, A. K., Rodriguez, A. C. & Osheroff, N. (2005). Human topoisomerase II-alpha rapidly relaxes positively supercoiled DNA: implications for enzyme action ahead of replication forks. Journal of Biological Chemistry 280, 39337–39345.CrossRefGoogle ScholarPubMed
McKay, D. B. & Steitz, T. A. (1981). Structure of catabolite gene activator protein at 2·9 Å resolution suggests binding to left-handed B-DNA. Nature 290, 744–749.CrossRefGoogle ScholarPubMed
Miki, Y., Chang, Z. T. & Horiuchi, T. (1984a). Control of cell division by sex factor F in Escherichia coli. II. Identification of genes for inhibitor protein and trigger protein on the 42·84–43·6 F segment. Journal of Molecular Biology 174, 627–646.CrossRefGoogle ScholarPubMed
Miki, Y., Yoshioka, K. & Horiuchi, T. (1984b). Control of cell division by sex factor F in Escherichia coli. I. The 42·84–43·6 F segment couples cell division of the host bacteria with replication of plasmid DNA. Journal of Molecular Biology 174, 605–625.CrossRefGoogle ScholarPubMed
Miller, K. G., Liu, L. F. & Englund, P. T. (1981). A homogeneous type II DNA topoisomerase from HeLa cell nuclei. Journal of Biological Chemistry 256, 9334–9339.CrossRefGoogle ScholarPubMed
Mirski, S. E., Gerlach, J. H., Cummings, H. J., Zirngibl, R., Greer, P. A. & Cole, S. P. (1997). Bipartite nuclear localization signals in the C terminus of human topoisomerase II alpha. Experimental Cell Research 237, 452–455.CrossRefGoogle Scholar
Mizuuchi, K., Fisher, L. M., O'Dea, M. H. & Gellert, M. (1980). DNA gyrase action involves the introduction of transient double-strand breaks into DNA. Proceedings of the National Academy of Sciences USA 77, 1847–1851.CrossRefGoogle ScholarPubMed
Mondragon, A. (2005). Unraveling the mechanistic details of topoisomerases. Structure 13, 502–503.CrossRefGoogle ScholarPubMed
Mondragon, A. & Digate, R. (1999). The structure of Escherichia coli DNA topoisomerase III. Structure 7, 1373–1383.CrossRefGoogle ScholarPubMed
Morais Cabral, J. H., Jackson, A. P., Smith, C. V., Shikotra, N., Maxwell, A. & Liddington, R. C. (1997). Crystal structure of the breakage–reunion domain of DNA gyrase. Nature 388, 903–906.CrossRefGoogle ScholarPubMed
Morris, S. K., Baird, C. L. & Lindsley, J. E. (2000). Steady-state and rapid kinetic analysis of topoisomerase II trapped as the closed-clamp intermediate by ICRF-193. Journal of Biological Chemistry 275, 2613–2618.CrossRefGoogle ScholarPubMed
Morrison, A. & Cozzarelli, N. R. (1979). Site-specific cleavage of DNA by E. coli DNA gyrase. Cell 17, 903–906.CrossRefGoogle ScholarPubMed
Mueller-Plantiz, F. & Herschlag, D. (2006). Interdomain communication in DNA topoisomerase II: DNA binding and enzyme activation. Journal of Biological Chemistry 281, 23395–23404.CrossRefGoogle Scholar
Mueller-Plantiz, F. & Herschlag, D. (2007). DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity. Nucleic Acids Research 35, 3764–3773.CrossRefGoogle Scholar
Nadal, M. (2007). Reverse gyrase: an insight into the role of DNA-topoisomerases. Biochimie 89, 447–455.CrossRefGoogle ScholarPubMed
Nakanishi, A., Oshida, T., Matsushita, T., Imajoh-Ohmi, S. & Ohnuki, T. (1998). Identification of DNA gyrase inhibitor (GyrI) in Escherichia coli. Journal of Biological Chemistry 273, 1933–1938.CrossRefGoogle ScholarPubMed
Nichols, M. D., Deangelis, K., Keck, J. L. & Berger, J. M. (1999). Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11. EMBO Journal 18, 6177–6188.CrossRefGoogle Scholar
Noble, C. G. & Maxwell, A. (2002). The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism. Journal of Molecular Biology 318, 361–371.CrossRefGoogle ScholarPubMed
Nollmann, M., Crisona, N. J. & Arimondo, P. B. (2007a). Thirty years of Escherichia coli DNA gyrase: from in vivo function to single-molecule mechanism. Biochimie 89, 490–499.CrossRefGoogle ScholarPubMed
Nollmann, M., Stone, M. D., Bryant, Z., Gore, J., Crisona, N. J., Hong, S. C., Mitelheiser, S., Maxwell, A., Bustamante, C. & Cozzarelli, N. R. (2007b). Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nature Structural and Molecular Biology 14, 264–271.CrossRefGoogle ScholarPubMed
Olland, S. & Wang, J. C. (1999). Catalysis of ATP hydrolysis by two NH(2)-terminal fragments of yeast DNA topoisomerase II. Journal of Biological Chemistry 274, 21688–21694.CrossRefGoogle ScholarPubMed
Oram, M., Travers, A. A., Howells, A. J., Maxwell, A. & Pato, M. L. (2006). Dissection of the bacteriophage Mu strong gyrase site (SGS): significance of the SGS right arm in Mu biology and DNA gyrase mechanism. Journal of Bacteriology 188, 619–632.CrossRefGoogle ScholarPubMed
Orphanides, G. & Maxwell, A. (1994). Evidence for a conformational change in the DNA gyrase–DNA complex from hydroxyl radical footprinting. Nucleic Acids Research 22, 1567–1575.CrossRefGoogle ScholarPubMed
Osheroff, N., Shelton, E. R. & Brutlag, D. L. (1983). DNA Topoisomerase II from Drosophila melanogaster. Journal of Biological Chemistry 258, 9563–9543.CrossRefGoogle ScholarPubMed
Pai, E. F., Kabsch, W., Krengel, U., Holmes, K. C., John, J. & Wittinghofer, A. (1989). Structure of the guanine-nucleotide-binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation. Nature 341, 209–214.CrossRefGoogle ScholarPubMed
Patel, A., Shuman, S. & Mondragon, A. (2006). Crystal structure of a bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA. Journal of Biological Chemistry 281, 6030–6037.CrossRefGoogle ScholarPubMed
Peak, M. J., Robb, F. T. & Peak, J. G. (1995). Extreme resistance to thermally induced DNA backbone breaks in the hyperthermophilic archaeon Pyrococcus furiosus. Journal of Bacteriology 177, 6316–6318.CrossRefGoogle ScholarPubMed
Peng, H. & Marians, K. J. (1993a). Decatenation activity of topoisomerase IV during oriC and pBR322 DNA replication in vitro. Proceedings of the National Academy of Sciences USA 90, 8571–8575.CrossRefGoogle ScholarPubMed
Peng, H. & Marians, K. J. (1993b). Escherichia coli topoisomerase IV. Purification, characterization, subunit structure, and subunit interactions. Journal of Biological Chemistry 268, 24481–24490.CrossRefGoogle ScholarPubMed
Peng, H. & Marians, K. J. (1995). The interaction of Escherichia coli topoisomerase IV with DNA. Journal of Biological Chemistry 270, 25286–25290.CrossRefGoogle ScholarPubMed
Perry, K., Hwang, Y., Bushman, F. D. & Van Duyne, G. D. (2006). Structural basis for specificity in the poxvirus topoisomerase. Molecular Cell 23, 343–354.CrossRefGoogle ScholarPubMed
Perry, K. & Mondragon, A. (2002). Biochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis. Journal of Biological Chemistry 277, 13237–13245.CrossRefGoogle ScholarPubMed
Perry, K. & Mondragon, A. (2003). Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA. Structure 11, 1349–1358.CrossRefGoogle ScholarPubMed
Peter, B. J., Ullsperger, C., Hiasa, H., Marians, K. J. & Cozzarelli, N. R. (1998). The structure of supercoiled intermediates in DNA replication. Cell 94, 819–827.CrossRefGoogle ScholarPubMed
Podtelezhnikov, A. A., Cozzarelli, N. R. & Vologodskii, A. (1999). Equilibrium distributions of topological states in circular DNA: interplay of supercoiling and knotting. Proceedings of the National Academy of Sciences USA 96, 12974–12979.CrossRefGoogle ScholarPubMed
Pommier, Y. (2006). Topoisomerase I inhibitors: camptothecins and beyond. Nature Reviews Cancer 6, 789–802.CrossRefGoogle ScholarPubMed
Pommier, Y. & Cherfils, J. (2005). Interfacial inhibition of macromolecular interactions: nature's paradigm for drug discovery. Trends in Pharmacological Sciences 26, 138–145.CrossRefGoogle ScholarPubMed
Pulleyblank, D. E., Shure, M., Tang, D., Vinograd, J. & Vosberg, H. P. (1975). Action of nicking–closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers. Proceedings of the National Academy of Sciences USA 72, 4280–4284.CrossRefGoogle ScholarPubMed
Pyle, A. M. (2008). Translocation and unwinding mechanisms of RNA and DNA helicases. Annual Reviews in Biophysics 37, 317–336.CrossRefGoogle ScholarPubMed
Qi, Y., Pei, J. & Grishin, N. V. (2000). C-terminal domain of gyrase A is predicted to have a beta-propeller structure. Proteins 47, 258–264.CrossRefGoogle Scholar
Raoult, D., Audic, S., Robert, C., Abergel, C., Renesto, P., Ogata, H., La Scola, B., Suzan, M. & Claverie, J. M. (2004). The 1·2-megabase genome sequence of Mimivirus. Science 306, 1344–1350.CrossRefGoogle ScholarPubMed
Redinbo, M. R., Champoux, J. J. & Hol, W. G. (2000). Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA. Biochemistry 39, 6832–6840.CrossRefGoogle ScholarPubMed
Redinbo, M. R., Stewart, L., Champoux, J. J. & Hol, W. G. (1999). Structural flexibility in human topoisomerase I revealed in multiple non-isomorphous crystal structures. Journal of Molecular Biology 292, 685–696.CrossRefGoogle ScholarPubMed
Redinbo, M. R., Stewart, L., Kuhn, P., Champoux, J. J. & Hol, W. G. (1998). Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 279, 1504–1513.CrossRefGoogle ScholarPubMed
Reece, R. J. & Maxwell, A. (1989). Tryptic fragments of the Escherichia coli DNA gyrase A protein. Journal of Biological Chemistry 264, 19648–19653.CrossRefGoogle ScholarPubMed
Reece, R. J. & Maxwell, A. (1991). The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein. Nucleic Acids Research 19, 1399–1405.CrossRefGoogle ScholarPubMed
Rhodes, D. & Klug, A. (1980). Helical periodicity of DNA determined by enzyme digestion. Nature 286, 573–578.CrossRefGoogle ScholarPubMed
Rice, P. A., Yang, S., Mizuuchi, K. & Nash, H. A. (1996). Crystal structure of an IHF–DNA complex: a protein-induced DNA U-turn. Cell 87, 1295–1306.CrossRefGoogle ScholarPubMed
Roca, J., Berger, J. M., Harrison, S. C. & Wang, J. C. (1996). DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism. Proceedings of the National Academy of Sciences USA 93, 4057–4062.CrossRefGoogle ScholarPubMed
Roca, J., Berger, J. M. & Wang, J. C. (1993a). On the simultaneous binding of eukaryotic DNA topoisomerase II to a pair of double-stranded DNA helices. Journal of Biological Chemistry 268, 14250–14255.CrossRefGoogle ScholarPubMed
Roca, J., Berger, J. M. & Wang, J. C. (1993b). On the simultaneous binding of eukaryotic DNA topoisomerase II to a pair of double-stranded DNA helices. Journal of Biological Chemistry 268, 14250–14255.CrossRefGoogle ScholarPubMed
Roca, J., Ishida, R., Berger, J. M., Andoh, T. & Wang, J. C. (1994). Antitumor bisdioxopiperazines inhibit yeast DNA topoisomerase II by trapping the enzyme in the form of a closed protein clamp. Proceedings of the National Academy of Sciences USA 91, 1781–1785.CrossRefGoogle ScholarPubMed
Roca, J. & Wang, J. C. (1992). The capture of a DNA double helix by an ATP-dependent protein clamp: a key state in DNA transport by type II DNA topoisomerases. Cell 71, 833–840.CrossRefGoogle Scholar
Roca, J. & Wang, J. C. (1994). DNA transport by a type II DNA topoisomerase: evidence in favor of a two-gate mechanism. Cell 77, 609–616.CrossRefGoogle ScholarPubMed
Roca, J. & Wang, J. C. (1996). The probabilities of supercoil removal and decatenation by yeast DNA topoisomerase II. Genes Cells 1, 17–27.CrossRefGoogle ScholarPubMed
Rodriguez, A. C. (2002). Studies of a positive supercoiling machine. Nucleotide hydrolysis and a multifunctional ‘latch’ in the mechanism of reverse gyrase. Journal of Biological Chemistry 277, 29865–29873.Google Scholar
Rodriguez, A. C. (2003). Investigating the role of the latch in the positive supercoiling mechanism of reverse gyrase. Biochemistry 42, 5993–6004.CrossRefGoogle ScholarPubMed
Rodriguez, A. C. & Stock, D. (2002). Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA. EMBO Journal 21, 418–426.CrossRefGoogle ScholarPubMed
Ruthenburg, A. J., Graybosch, D. M., Huetsch, J. C. & Verdine, G. L. (2005). A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. Journal of Biological Chemistry 280, 26177–26184.CrossRefGoogle ScholarPubMed
Rybenkov, V. V., Ullsperger, C., Vologodskii, A. V. & Cozzarelli, N. R. (1997). Simplification of DNA topology below equilibrium values by type II topoisomerases. Science 277, 690–693.CrossRefGoogle ScholarPubMed
Sander, M. & Hsieh, T. (1983). Double strand DNA cleavage by type II DNA topoisomerase from Drosophila melanogaster. Journal of Biological Chemistry 258, 8421–8428.CrossRefGoogle ScholarPubMed
Sari, L. & Andricioaei, I. (2005). Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation. Nucleic Acids Research 33, 6621–6634.CrossRefGoogle ScholarPubMed
Schultz, P., Olland, S., Oudet, P. & Hancock, R. (1996). Structure and conformational changes of DNA topoisomerase II visualized by electron microscopy. Proceedings of the National Academy of Sciences USA 93, 5936–5940.CrossRefGoogle ScholarPubMed
Sengupta, S., Shah, M. & Nagaraja, V. (2006). Glutamate racemase from Mycobacterium tuberculosis inhibits DNA gyrase by affecting its DNA-binding. Nucleic Acids Research 34, 5567–5576.CrossRefGoogle ScholarPubMed
Shuman, S. & Prescott, J. (1990). Specific DNA cleavage and binding by vaccinia virus DNA topoisomerase I. Journal of Biological Chemistry 265, 17826–17836.CrossRefGoogle ScholarPubMed
Singleton, M. A., Dillingham, M. S. & Wigley, D. B. (2007). Structure and mechanism of helicases and nucleic acid translocases. Annual Review of Biochemistry 76, 23–50.CrossRefGoogle ScholarPubMed
Sioud, M., Possot, O., Elie, C., Sibold, L. & Forterre, P. (1988). Coumarin and quinolone action in archaebacteria: evidence for the presence of a DNA gyrase-like enzyme. Journal of Bacteriology 70, 946–953.CrossRefGoogle Scholar
Slesarev, A. I., Stetter, K. O., Lake, J. A., Gellert, M., Krah, R. & Kozyavkin, S. A. (1993). DNA topoisomerase V is a relative of eukaryotic topoisomerase I from a hyperthermophilic prokaryote. Nature 364, 735–737.CrossRefGoogle ScholarPubMed
Slesarev, A. I., Zaitzev, D. A., Kopylov, V. M., Stetter, K. O. & Kozyavkin, S. A. (1991). DNA topoisomerase III from extremely thermophilic archaebacteria. ATP-independent type I topoisomerase from Desulfurococcus amylolyticus drives extensive unwinding of closed circular DNA at high temperature. Journal of Biological Chemistry 266, 12321–12328.CrossRefGoogle ScholarPubMed
Smiley, R. D., Collins, T. R. L., Hammes, G. G. & Hsieh, T.-S. (2007). Single-molecule measurements of the opening and closing of the DNA gate by eukaryotic topoisomerase II. Proceedings of the National Academy of Sciences USA 104, 4840–4845.CrossRefGoogle ScholarPubMed
Smith, A. B. & Maxwell, A. (2006). A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site. Nucleic Acids Research 34, 4667–4676.CrossRefGoogle ScholarPubMed
Srivenugopal, K. S., Lockshon, D. & Morris, D. R. (1984). Escherichia coli DNA topoisomerase III: purification and characterization of a new type I enzyme. Biochemistry 23, 1899–1906.CrossRefGoogle ScholarPubMed
Staker, B. L., Hjerrild, K., Feese, M. D., Behnke, C. A., Burgin, A. B. Jr. & Stewart, L. (2002). The mechanism of topoisomerase I poisoning by a camptothecin analog. Proceedings of the National Academy of Sciences USA 99, 15387–15392.CrossRefGoogle ScholarPubMed
Stetler, G. L., King, G. J. & Huang, W. M. (1979). T4 DNA-delay proteins requires for specific DNA replication form a complex that has ATP-dependent topoisomerase activity. Proceedings of the National Academy of Sciences USA 76, 3737–3741.CrossRefGoogle Scholar
Stewart, L., Ireton, G. C. & Champoux, J. J. (1996). The domain organization of human topoisomerase I. Journal of Biological Chemistry 271, 7602–7608.CrossRefGoogle ScholarPubMed
Stewart, L., Ireton, G. C. & Champoux, J. J. (1997). Reconstitution of human topoisomerase I by fragment complementation. Journal of Molecular Biology 269, 355–372.CrossRefGoogle ScholarPubMed
Stewart, L., Ireton, G. C. & Champoux, J. J. (1999). A functional linker in human topoisomerase I is required for maximum sensitivity to camptothecin in a DNA relaxation assay. Journal of Biological Chemistry 274, 32950–32960.CrossRefGoogle Scholar
Stewart, L., Redinbo, M. R., Qiu, X., Hol, W. G. & Champoux, J. J. (1998). A model for the mechanism of human topoisomerase I. Science 279, 1534–1541.CrossRefGoogle Scholar
Stivers, J. T., Harris, T. K. & Mildvan, A. S. (1997). Vaccinia DNA topoisomerase I: evidence supporting a free rotation mechanism for DNA supercoil relaxation. Biochemistry 36, 5212–5222.CrossRefGoogle ScholarPubMed
Stone, M. D., Bryant, Z., Crisona, N. J., Smith, S. B., Vologodskii, A., Bustamante, C. & Cozzarelli, N. R. (2003). Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proceedings of the National Academy of Sciences USA 100, 8654–8659.CrossRefGoogle ScholarPubMed
Story, R. M. & Steitz, T. A. (1992). Structure of the recA protein–ADP complex. Nature 355, 374–376.CrossRefGoogle ScholarPubMed
Sugimoto-Shirasu, K., Roberts, G. R., Stacey, N. J., McCann, M. C. & Maxwell, A. (2005). RHL1 is an essential component of the plant DNA topoisomerase VI complex and is required for ploidy-dependent cell growth. Proceedings of the National Academy of Sciences USA 102, 18736–18741.CrossRefGoogle ScholarPubMed
Sugino, A., Higgins, N. P. & Cozzarelli, N. R. (1980). DNA gyrase subunit stoichiometry and the covalent attachment of subunit A to DNA during DNA cleavage. Nucleic Acids Research 8, 3865–3874.CrossRefGoogle Scholar
Taneja, B., Patel, A., Slesarev, A. & Mondragon, A. (2006). Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases. EMBO Journal 25, 398–408.CrossRefGoogle ScholarPubMed
Taneja, B., Schnurr, B., Slesarev, A., Marko, J. F. & Mondragon, A. (2007). Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism. Proceedings of the National Academy of Sciences USA 104, 14670–14675.CrossRefGoogle ScholarPubMed
Thompson, R. J. & Mosig, G. (1985). An ATP-dependent supercoiling topoisomerase of Chlamydomonas reinhardtii affects accumulation of specific chloroplast transcripts. Nucleic Acids Research 13, 873–891.CrossRefGoogle ScholarPubMed
Thomsen, B., Bendixen, C., Lund, K., Anderson, A. H., Sorensen, B. S. & Westergaard, O. (1990). Characterization of the interaction between topoisomerase II and DNA by transcriptional footprinting. Journal of Molecular Biology 215, 237–244.CrossRefGoogle ScholarPubMed
Tian, L., Claeboe, C. D., Hecht, S. M. & Shuman, S. (2004). Remote phosphate contacts trigger assembly of the active site of DNA topoisomerase IB. Structure 12, 31–40.CrossRefGoogle ScholarPubMed
Tian, L., Claeboe, C. D., Hecht, S. M. & Shuman, S. (2005). Mechanistic plasticity of DNA topoisomerase IB: phosphate electrostatics dictate the need for a catalytic arginine. Structure 13, 513–520.CrossRefGoogle ScholarPubMed
Tingey, A. P. & Maxwell, A. (1996). Probing the role of the ATP-operated clamp in the strand-passage reaction of DNA gyrase. Nucleic Acids Research 24, 4868–4873.CrossRefGoogle ScholarPubMed
Tran, J. H. & Jacoby, G. A. (2002). Mechanism of plasmid-mediated quinolone resistance. Proceedings of the National Academy of Sciences USA 99, 5638–5642.CrossRefGoogle ScholarPubMed
Trigueros, S., Salceda, J., Bermudez, I., Fernandez, X. & Roca, J. (2004). Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology. Journal of Molecular Biology 335, 723–731.CrossRefGoogle ScholarPubMed
Tse, Y. C., Kirkegaard, K. & Wang, J. C. (1980). Covalent bonds between protein and DNA. Formation of phosphotyrosine linkage between certain DNA topoisomerases and DNA. Journal of Biological Chemistry 255, 5560–5565.CrossRefGoogle ScholarPubMed
Tse-Dinh, Y. C. & Beran-Steed, R. K. (1988). Escherichia coli DNA topoisomerase I is a zinc metalloprotein with three repetitive zinc-binding domains. Journal of Biological Chemistry 263, 15857–15859.CrossRefGoogle ScholarPubMed
Vinograd, J., Lebowitz, J., Radloff, R., Watson, R. & Laipis, P. (1965). The twisted circular form of polynoma viral DNA. Proceedings of the National Academy of Sciences USA 53, 1104–1111.CrossRefGoogle Scholar
Vologodskii, A. V. & Cozzarelli, N. R. (1994). Conformational and thermodynamic properties of supercoiled DNA. Annual Review of Biophysics and Biomolecular Structure 23, 609–643.CrossRefGoogle ScholarPubMed
Vologodskii, A. V., Zhang, W., Rybenkov, V. V., Podtelezhnikov, A. A., Subramanian, D., Griffith, J. D. & Cozzarelli, N. R. (2001). Mechanism of topology simplification by type II DNA topoisomerases. Proceedings of the National Academy of Sciences USA 98, 3045–3049.CrossRefGoogle ScholarPubMed
Wallis, J. W., Chrebet, G., Brodsky, G., Rolfe, M. & Rothstein, R. (1989). A hyper-recombination mutation in S. cerevisiae identifies a novel eukaryotic topoisomerase. Cell 58, 409–419.CrossRefGoogle Scholar
Wang, J. C. (1971). Interaction between DNA and an Escherichia coli protein omega. Journal of Molecular Biology 55, 523–533.CrossRefGoogle Scholar
Wang, J. C. (1998). Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine. Quarterly Review of Biophysics 31, 107–144.CrossRefGoogle ScholarPubMed
Wang, J. C. (2002). Cellular roles of DNA topoisomerases: a molecular perspective. Nature Reviews Molecular and Cellular Biology 3, 430–440.CrossRefGoogle ScholarPubMed
Wang, J. C. (2007). Unlocking and opening a DNA gate. Proceedings of the National Academy of Sciences USA 104, 4773–4774.CrossRefGoogle ScholarPubMed
Wang, J. C. & Kirkegaard, K. (1981). DNA topoisomerases. Gene Amplification and Analysis 2, 455–473.Google ScholarPubMed
Wang, S. C. & Shapiro, L. (2004). The topoisomerase IV ParC subunit colocalizes with the Caulobacter replisome and is required for polar localization of replication origins. Proceedings of the National Academy of Sciences USA 101, 9251–9256.CrossRefGoogle ScholarPubMed
Ward, D. & Newton, A. (1997). Requirement of topoisomerase IV parC and parE genes for cell cycle progression and developmental regulation in Caulobacter crescentus. Molecular Microbiology 26, 897–910.CrossRefGoogle ScholarPubMed
Wei, H., Ruthenburg, A. J., Bechis, S. K. & Verdine, G. L. (2005). Nucleotide-dependent domain movement in the ATPase domain of a human type IIA DNA topoisomerase. Journal of Biological Chemistry 280, 37041–37047.CrossRefGoogle ScholarPubMed
West, K. L., Meczes, E. L., Thorn, R., Turnbull, R. M., Marshall, R. & Austin, C. A. (2000). Mutagenesis of E477 or K505 in the B′ domain of human topoisomerase II beta increases the requirement for magnesium ions during strand passage. Biochemistry 39, 1223–1233.CrossRefGoogle ScholarPubMed
White, J. H. (1969). Self-linking and the Gauss integral in higher dimensions. American Journal of Mathematics 91, 693–728.CrossRefGoogle Scholar
Wigley, D. B., Davies, G. J., Dodson, E. J., Maxwell, A. & Dodson, G. (1991). Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 351, 624–629.CrossRefGoogle ScholarPubMed
Williams, N. L. & Maxwell, A. (1999). Probing the two-gate mechanism of DNA gyrase using cysteine cross-linking. Biochemistry 38, 13502–13511.CrossRefGoogle ScholarPubMed
Woessner, R. D., Mattern, M. R., Mirabelli, C. K., Johnson, R. K. & Drake, F. H. (1991). Proliferation- and cell cycle-dependent differences in expression of the 170 kilodalton and 180 kilodalton forms of topoisomerase II in NIH-3T3 cells. Cell Growth and Differentiation 2, 209–214.Google ScholarPubMed
Woo, M. H., Losasso, C., Guo, H., Pattarello, L., Benedetti, P. & Bjornsti, M. A. (2003). Locking the DNA topoisomerase I protein clamp inhibits DNA rotation and induces cell lethality. Proceedings of the National Academy of Sciences USA 100, 13767–13772.CrossRefGoogle ScholarPubMed
Wu, H. Y., Shyy, S. H., Wang, J. C. & Liu, L. F. (1988). Transcription generates positively and negatively supercoiled domains in the template. Cell 53, 433–440.CrossRefGoogle ScholarPubMed
Wu, L., Bachrati, C. Z., Ou, J., Xu, C., Yin, J., Chang, M., Wang, W., Li, L., Brown, G. W. & Hickson, I. D. (2006). BLAP75/RMI1 promotes the BLM-dependent dissolution of homologous recombination intermediates. Proceedings of the National Academy of Sciences USA 103, 4068–4073.CrossRefGoogle ScholarPubMed
Wu, L., Davies, S. L., North, P. S., Goulaouic, H., Riou, J. F., Turley, H., Gatter, K. C. & Hickson, I. D. (2000). The Bloom's syndrome gene product interacts with topoisomerase III. Journal of Biological Chemistry 275, 9636–9644.CrossRefGoogle ScholarPubMed
Yakovleva, L., Chen, S., Hecht, S. M. & Shuman, S. (2008). Chemical and traditional mutagenesis of vaccinia DNA topoisomerase provide insights to cleavage site recognition and transesterification chemistry. Journal of Biological Chemistry.CrossRefGoogle ScholarPubMed
Yamane, K., Kawabata, M. & Tsuruo, T. (1997). A DNA-topoisomerase-II-binding protein with eight repeating regions similar to DNA-repair enzymes and to a cell-cycle regulator. European Journal of Biochemistry 250, 794–799.CrossRefGoogle ScholarPubMed
Yan, J., Magnasco, M. O. & Marko, J. F. (2001). Kinetic proofreading can explain the suppression of supercoiling of circular DNA molecules by type-II topoisomerases. Physical Review E, Statistical and Nonlinear Soft Matter Physics 63, 031909.CrossRefGoogle ScholarPubMed
Yang, X., Li, W., Prescott, E. D., Burden, S. J. & Wang, J. C. (2000). DNA topoisomerase IIbeta and neural development. Science 287, 131–134.CrossRefGoogle ScholarPubMed
Yu, G. W., Allen, M. D., Andreeva, A., Fersht, A. R. & Bycroft, M. (2006). Solution structure of the C4 zinc finger domain of HDM2. Protein Science 15, 384–389.CrossRefGoogle ScholarPubMed
Yu, L., Zhu, C. X., Tse-Dinh, Y. C. & Fesik, S. W. (1995). Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I. Biochemistry 34, 7622–7628.CrossRefGoogle ScholarPubMed
Zechiedrich, E. L., Khodursky, A. B., Bachellier, S., Schneider, R., Chen, D., Lilley, D. M. & Cozzarelli, N. R. (2000). Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. Journal of Biological Chemistry 275, 8103–8113.CrossRefGoogle ScholarPubMed
Zechiedrich, E. L., Khodursky, A. B. & Cozzarelli, N. R. (1997). Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli. Genes and Development 11, 2580–2592.CrossRefGoogle Scholar
Zechiedrich, E. L. & Osheroff, N. (1990a). Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers. EMBO Journal 9, 4555–4562.CrossRefGoogle ScholarPubMed
Zechiedrich, E. L. & Osheroff, N. (1990b). Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers. EMBO Journal 9, 4555–4562.CrossRefGoogle ScholarPubMed
Zhu, C. X., Roche, C. J., Papanicolaou, N., Dipietrantonio, A. & Tse-Dinh, Y. C. (1998). Site-directed mutagenesis of conserved aspartates, glutamates and arginines in the active site region of Escherichia coli DNA topoisomerase I. Journal of Biological Chemistry 273, 8783–8789.CrossRefGoogle ScholarPubMed
Zhu, C. X. & Tse-Dinh, Y. C. (2000). The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change. Journal of Biological Chemistry 275, 5318–5322.CrossRefGoogle ScholarPubMed