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Volumn 16, Issue 1, 2014, Pages 23-34

The mechanism of negative DNA supercoiling: A cascade of DNA-induced conformational changes prepares gyrase for strand passage

Author keywords

ATP driven conformational changes; DNA topology; Molecular machine; Negative supercoiling; Strand passage; Topoisomerase mechanism

Indexed keywords

ATP-DRIVEN CONFORMATIONAL CHANGES; DNA TOPOLOGY; MOLECULAR MACHINE; NEGATIVE SUPERCOILING; STRAND PASSAGE; TOPOISOMERASE MECHANISM;

EID: 84894348243     PISSN: 15687864     EISSN: 15687856     Source Type: Journal    
DOI: 10.1016/j.dnarep.2014.01.011     Document Type: Article
Times cited : (32)

References (92)
  • 1
    • 0016638632 scopus 로고
    • Thermodynamic properties of superhelical DNAs
    • Hsieh T.S., Wang J.C. Thermodynamic properties of superhelical DNAs. Biochemistry 1975, 14:527-535.
    • (1975) Biochemistry , vol.14 , pp. 527-535
    • Hsieh, T.S.1    Wang, J.C.2
  • 2
    • 0023433855 scopus 로고
    • Supercoiling of the DNA template during transcription
    • Liu L.F., Wang J.C. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. U. S. A. 1987, 84:7024-7027.
    • (1987) Proc. Natl. Acad. Sci. U. S. A. , vol.84 , pp. 7024-7027
    • Liu, L.F.1    Wang, J.C.2
  • 3
    • 0017055337 scopus 로고
    • Formation of catenated molecules by replication of colicin E1 plasmid DNA in cell extracts
    • Sakakibara Y., Suzuki K., Tomizawa J.I. Formation of catenated molecules by replication of colicin E1 plasmid DNA in cell extracts. J. Mol. Biol. 1976, 108:569-582.
    • (1976) J. Mol. Biol. , vol.108 , pp. 569-582
    • Sakakibara, Y.1    Suzuki, K.2    Tomizawa, J.I.3
  • 5
    • 50649101663 scopus 로고    scopus 로고
    • DNA topoisomerases: harnessing and constraining energy to govern chromosome topology
    • Schoeffler A.J., Berger J.M. DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Q. Rev. Biophys. 2008, 41:41-101.
    • (2008) Q. Rev. Biophys. , vol.41 , pp. 41-101
    • Schoeffler, A.J.1    Berger, J.M.2
  • 6
    • 0017844753 scopus 로고
    • Interaction between DNA and Escherichia coli protein omega. Formation of a complex between single-stranded DNA and omega protein
    • Depew R.E., Liu L.F., Wang J.C. Interaction between DNA and Escherichia coli protein omega. Formation of a complex between single-stranded DNA and omega protein. J. Biol. Chem. 1978, 253:511-518.
    • (1978) J. Biol. Chem. , vol.253 , pp. 511-518
    • Depew, R.E.1    Liu, L.F.2    Wang, J.C.3
  • 7
    • 0018572806 scopus 로고
    • Interaction between DNA and Escherichia coli DNA topoisomerase I. Formation of complexes between the protein and superhelical and nonsuperhelical duplex DNAs
    • Liu L.F., Wang J.C. Interaction between DNA and Escherichia coli DNA topoisomerase I. Formation of complexes between the protein and superhelical and nonsuperhelical duplex DNAs. J. Biol. Chem. 1979, 254:11082-11088.
    • (1979) J. Biol. Chem. , vol.254 , pp. 11082-11088
    • Liu, L.F.1    Wang, J.C.2
  • 8
    • 0019332581 scopus 로고
    • Covalent bonds between protein and DNA. Formation of phosphotyrosine linkage between certain DNA topoisomerases and DNA
    • Tse Y.C., Kirkegaard K., Wang J.C. Covalent bonds between protein and DNA. Formation of phosphotyrosine linkage between certain DNA topoisomerases and DNA. J. Biol. Chem. 1980, 255:5560-5565.
    • (1980) J. Biol. Chem. , vol.255 , pp. 5560-5565
    • Tse, Y.C.1    Kirkegaard, K.2    Wang, J.C.3
  • 9
    • 0019888076 scopus 로고
    • DNA is linked to the rat liver DNA nicking-closing enzyme by a phosphodiester bond to tyrosine
    • Champoux J.J. DNA is linked to the rat liver DNA nicking-closing enzyme by a phosphodiester bond to tyrosine. J. Biol. Chem. 1981, 256:4805-4809.
    • (1981) J. Biol. Chem. , vol.256 , pp. 4805-4809
    • Champoux, J.J.1
  • 10
    • 0034923502 scopus 로고    scopus 로고
    • DNA topoisomerases: structure, function, and mechanism
    • Champoux J.J. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 2001, 70:369-413.
    • (2001) Annu. Rev. Biochem. , vol.70 , pp. 369-413
    • Champoux, J.J.1
  • 11
    • 0021154312 scopus 로고
    • Reverse gyrase - a topoisomerase which introduces positive superhelical turns into DNA
    • Kikuchi A., Asai K. Reverse gyrase - a topoisomerase which introduces positive superhelical turns into DNA. Nature 1984, 309:677-681.
    • (1984) Nature , vol.309 , pp. 677-681
    • Kikuchi, A.1    Asai, K.2
  • 12
    • 3142753959 scopus 로고    scopus 로고
    • Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling
    • Kampmann M., Stock D. Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling. Nucleic Acids Res. 2004, 32:3537-3545.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3537-3545
    • Kampmann, M.1    Stock, D.2
  • 13
    • 33646832425 scopus 로고    scopus 로고
    • Reverse gyrase functions as a DNA renaturase: annealing of complementary single-stranded circles and positive supercoiling of a bubble substrate
    • Hsieh T.S., Plank J.L. Reverse gyrase functions as a DNA renaturase: annealing of complementary single-stranded circles and positive supercoiling of a bubble substrate. J. Biol. Chem. 2006, 281:5640-5647.
    • (2006) J. Biol. Chem. , vol.281 , pp. 5640-5647
    • Hsieh, T.S.1    Plank, J.L.2
  • 15
    • 0031006668 scopus 로고    scopus 로고
    • Vaccinia DNA topoisomerase I: evidence supporting a free rotation mechanism for DNA supercoil relaxation
    • Stivers J.T., Harris T.K., Mildvan A.S. Vaccinia DNA topoisomerase I: evidence supporting a free rotation mechanism for DNA supercoil relaxation. Biochemistry 1997, 36:5212-5222.
    • (1997) Biochemistry , vol.36 , pp. 5212-5222
    • Stivers, J.T.1    Harris, T.K.2    Mildvan, A.S.3
  • 16
    • 0023654375 scopus 로고
    • Mapping the active site tyrosine of Escherichia coli DNA gyrase
    • Horowitz D.S., Wang J.C. Mapping the active site tyrosine of Escherichia coli DNA gyrase. J. Biol. Chem. 1987, 262:5339-5344.
    • (1987) J. Biol. Chem. , vol.262 , pp. 5339-5344
    • Horowitz, D.S.1    Wang, J.C.2
  • 17
    • 0018666498 scopus 로고
    • A sign inversion mechanism for enzymatic supercoiling of DNA
    • Brown P.O., Cozzarelli N.R. A sign inversion mechanism for enzymatic supercoiling of DNA. Science 1979, 206:1081-1083.
    • (1979) Science , vol.206 , pp. 1081-1083
    • Brown, P.O.1    Cozzarelli, N.R.2
  • 18
    • 0018422012 scopus 로고
    • Site-specific cleavage of DNA by E. coli DNA gyrase
    • Morrison A., Cozzarelli N.R. Site-specific cleavage of DNA by E. coli DNA gyrase. Cell 1979, 17:175-184.
    • (1979) Cell , vol.17 , pp. 175-184
    • Morrison, A.1    Cozzarelli, N.R.2
  • 20
    • 0031695155 scopus 로고    scopus 로고
    • Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine
    • Wang J.C. Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine. Q. Rev. Biophys. 1998, 31:107-144.
    • (1998) Q. Rev. Biophys. , vol.31 , pp. 107-144
    • Wang, J.C.1
  • 21
    • 0030987132 scopus 로고    scopus 로고
    • An atypical topoisomerase II from Archaea with implications for meiotic recombination
    • Bergerat A., de Massy B., Gadelle D., Varoutas P.C., Nicolas A., Forterre P. An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature 1997, 386:414-417.
    • (1997) Nature , vol.386 , pp. 414-417
    • Bergerat, A.1    de Massy, B.2    Gadelle, D.3    Varoutas, P.C.4    Nicolas, A.5    Forterre, P.6
  • 22
    • 0000800913 scopus 로고
    • Catenation and knotting of duplex DNA by type 1 topoisomerases: a mechanistic parallel with type 2 topoisomerases
    • Brown P.O., Cozzarelli N.R. Catenation and knotting of duplex DNA by type 1 topoisomerases: a mechanistic parallel with type 2 topoisomerases. Proc. Natl. Acad. Sci. U. S. A. 1981, 78:843-847.
    • (1981) Proc. Natl. Acad. Sci. U. S. A. , vol.78 , pp. 843-847
    • Brown, P.O.1    Cozzarelli, N.R.2
  • 23
    • 0033550077 scopus 로고    scopus 로고
    • Probing the two-gate mechanism of DNA gyrase using cysteine cross-linking
    • Williams N.L., Maxwell A. Probing the two-gate mechanism of DNA gyrase using cysteine cross-linking. Biochemistry 1999, 38:13502-13511.
    • (1999) Biochemistry , vol.38 , pp. 13502-13511
    • Williams, N.L.1    Maxwell, A.2
  • 24
    • 0035830951 scopus 로고    scopus 로고
    • Locking the ATP-operated clamp of DNA gyrase: probing the mechanism of strand passage
    • Williams N.L., Howells A.J., Maxwell A. Locking the ATP-operated clamp of DNA gyrase: probing the mechanism of strand passage. J. Mol. Biol. 2001, 306:969-984.
    • (2001) J. Mol. Biol. , vol.306 , pp. 969-984
    • Williams, N.L.1    Howells, A.J.2    Maxwell, A.3
  • 25
    • 0033607152 scopus 로고    scopus 로고
    • Locking the DNA gate of DNA gyrase: investigating the effects on DNA cleavage and ATP hydrolysis
    • Williams N.L., Maxwell A. Locking the DNA gate of DNA gyrase: investigating the effects on DNA cleavage and ATP hydrolysis. Biochemistry 1999, 38:14157-14164.
    • (1999) Biochemistry , vol.38 , pp. 14157-14164
    • Williams, N.L.1    Maxwell, A.2
  • 26
    • 0018731640 scopus 로고
    • T4 DNA topoisomerase: a new ATP-dependent enzyme essential for initiation of T4 bacteriophage DNA replication
    • Liu L.F., Liu C.C., Alberts B.M. T4 DNA topoisomerase: a new ATP-dependent enzyme essential for initiation of T4 bacteriophage DNA replication. Nature 1979, 281:456-461.
    • (1979) Nature , vol.281 , pp. 456-461
    • Liu, L.F.1    Liu, C.C.2    Alberts, B.M.3
  • 27
    • 0018306971 scopus 로고
    • T4 DNA-delay proteins, required for specific DNA replication, form a complex that has ATP-dependent DNA topoisomerase activity
    • Stetler G.L., King G.J., Huang W.M. T4 DNA-delay proteins, required for specific DNA replication, form a complex that has ATP-dependent DNA topoisomerase activity. Proc. Natl. Acad. Sci. U. S. A. 1979, 76:3737-3741.
    • (1979) Proc. Natl. Acad. Sci. U. S. A. , vol.76 , pp. 3737-3741
    • Stetler, G.L.1    King, G.J.2    Huang, W.M.3
  • 29
    • 0022423155 scopus 로고
    • An ATP-dependent supercoiling topoisomerase of Chlamydomonas reinhardtii affects accumulation of specific chloroplast transcripts
    • Thompson R.J., Mosig G. An ATP-dependent supercoiling topoisomerase of Chlamydomonas reinhardtii affects accumulation of specific chloroplast transcripts. Nucleic Acids Res. 1985, 13:873-891.
    • (1985) Nucleic Acids Res. , vol.13 , pp. 873-891
    • Thompson, R.J.1    Mosig, G.2
  • 30
    • 0023955608 scopus 로고
    • Coumarin and quinolone action in archaebacteria: evidence for the presence of a DNA gyrase-like enzyme
    • Sioud M., Possot O., Elie C., Sibold L., Forterre P. Coumarin and quinolone action in archaebacteria: evidence for the presence of a DNA gyrase-like enzyme. J. Bacteriol. 1988, 170:946-953.
    • (1988) J. Bacteriol. , vol.170 , pp. 946-953
    • Sioud, M.1    Possot, O.2    Elie, C.3    Sibold, L.4    Forterre, P.5
  • 31
    • 0018628599 scopus 로고
    • Escherichia coli mutants thermosensitive for deoxyribonucleic acid gyrase subunit A: effects on deoxyribonucleic acid replication, transcription, and bacteriophage growth
    • Kreuzer K.N., Cozzarelli N.R. Escherichia coli mutants thermosensitive for deoxyribonucleic acid gyrase subunit A: effects on deoxyribonucleic acid replication, transcription, and bacteriophage growth. J. Bacteriol. 1979, 140:424-435.
    • (1979) J. Bacteriol. , vol.140 , pp. 424-435
    • Kreuzer, K.N.1    Cozzarelli, N.R.2
  • 32
    • 0021112063 scopus 로고
    • Positively supercoiled plasmid DNA is produced by treatment of Escherichia coli with DNA gyrase inhibitors
    • Lockshon D., Morris D.R. Positively supercoiled plasmid DNA is produced by treatment of Escherichia coli with DNA gyrase inhibitors. Nucleic Acids Res. 1983, 11:2999-3017.
    • (1983) Nucleic Acids Res. , vol.11 , pp. 2999-3017
    • Lockshon, D.1    Morris, D.R.2
  • 33
    • 77954187741 scopus 로고    scopus 로고
    • DNA topoisomerases and their poisoning by anticancer and antibacterial drugs
    • Pommier Y., Leo E., Zhang H., Marchand C. DNA topoisomerases and their poisoning by anticancer and antibacterial drugs. Chem. Biol. 2010, 17:421-433.
    • (2010) Chem. Biol. , vol.17 , pp. 421-433
    • Pommier, Y.1    Leo, E.2    Zhang, H.3    Marchand, C.4
  • 34
    • 82355173219 scopus 로고    scopus 로고
    • Exploiting bacterial DNA gyrase as a drug target: current state and perspectives
    • Collin F., Karkare S., Maxwell A. Exploiting bacterial DNA gyrase as a drug target: current state and perspectives. Appl. Microbiol. Biotechnol. 2011, 92:479-497.
    • (2011) Appl. Microbiol. Biotechnol. , vol.92 , pp. 479-497
    • Collin, F.1    Karkare, S.2    Maxwell, A.3
  • 35
    • 0033985080 scopus 로고    scopus 로고
    • GHKL, an emergent ATPase/kinase superfamily
    • Dutta R., Inouye M. GHKL, an emergent ATPase/kinase superfamily. Trends Biochem. Sci. 2000, 25:24-28.
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 24-28
    • Dutta, R.1    Inouye, M.2
  • 36
    • 0026428621 scopus 로고
    • Crystal structure of an N-terminal fragment of the DNA gyrase B protein
    • Wigley D.B., Davies G.J., Dodson E.J., Maxwell A., Dodson G. Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 1991, 351:624-629.
    • (1991) Nature , vol.351 , pp. 624-629
    • Wigley, D.B.1    Davies, G.J.2    Dodson, E.J.3    Maxwell, A.4    Dodson, G.5
  • 37
    • 73149096968 scopus 로고    scopus 로고
    • Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation
    • Fu G., Wu J., Liu W., Zhu D., Hu Y., Deng J., Zhang X.E., Bi L., Wang D.C. Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation. Nucleic Acids Res. 2009, 37:5908-5916.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 5908-5916
    • Fu, G.1    Wu, J.2    Liu, W.3    Zhu, D.4    Hu, Y.5    Deng, J.6    Zhang, X.E.7    Bi, L.8    Wang, D.C.9
  • 39
    • 22544447404 scopus 로고    scopus 로고
    • A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias
    • Ruthenburg A.J., Graybosch D.M., Huetsch J.C., Verdine G.L. A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. J. Biol. Chem. 2005, 280:26177-26184.
    • (2005) J. Biol. Chem. , vol.280 , pp. 26177-26184
    • Ruthenburg, A.J.1    Graybosch, D.M.2    Huetsch, J.C.3    Verdine, G.L.4
  • 40
    • 78649879246 scopus 로고    scopus 로고
    • A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function
    • Schoeffler A.J., May A.P., Berger J.M. A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucleic Acids Res. 2010, 38:7830-7844.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 7830-7844
    • Schoeffler, A.J.1    May, A.P.2    Berger, J.M.3
  • 41
    • 0027419771 scopus 로고
    • The 43-kilodalton N-terminal fragment of the DNA gyrase B protein hydrolyzes ATP and binds coumarin drugs
    • Ali J.A., Jackson A.P., Howells A.J., Maxwell A. The 43-kilodalton N-terminal fragment of the DNA gyrase B protein hydrolyzes ATP and binds coumarin drugs. Biochemistry 1993, 32:2717-2724.
    • (1993) Biochemistry , vol.32 , pp. 2717-2724
    • Ali, J.A.1    Jackson, A.P.2    Howells, A.J.3    Maxwell, A.4
  • 42
    • 0026448670 scopus 로고
    • The capture of a DNA double helix by an Atp-dependent protein clamp - a key step in DNA transport by type-Ii DNA topoisomerases
    • Roca J., Wang J.C. The capture of a DNA double helix by an Atp-dependent protein clamp - a key step in DNA transport by type-Ii DNA topoisomerases. Cell 1992, 71:833-840.
    • (1992) Cell , vol.71 , pp. 833-840
    • Roca, J.1    Wang, J.C.2
  • 43
    • 80052181150 scopus 로고    scopus 로고
    • DNA-induced narrowing of the gyrase N-gate coordinates T-segment capture and strand passage
    • Gubaev A., Klostermeier D. DNA-induced narrowing of the gyrase N-gate coordinates T-segment capture and strand passage. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:14085-14090.
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , pp. 14085-14090
    • Gubaev, A.1    Klostermeier, D.2
  • 44
  • 45
    • 33645652225 scopus 로고    scopus 로고
    • The GyrA-box is required for the ability of DNA gyrase to wrap DNA and catalyze the supercoiling reaction
    • Kramlinger V.M., Hiasa H. The GyrA-box is required for the ability of DNA gyrase to wrap DNA and catalyze the supercoiling reaction. J. Biol. Chem. 2006, 281:3738-3742.
    • (2006) J. Biol. Chem. , vol.281 , pp. 3738-3742
    • Kramlinger, V.M.1    Hiasa, H.2
  • 46
    • 0030664213 scopus 로고    scopus 로고
    • Requirement of topoisomerase IV parC and parE genes for cell cycle progression and developmental regulation in Caulobacter crescentus
    • Ward D., Newton A. Requirement of topoisomerase IV parC and parE genes for cell cycle progression and developmental regulation in Caulobacter crescentus. Mol. Microbiol. 1997, 26:897-910.
    • (1997) Mol. Microbiol. , vol.26 , pp. 897-910
    • Ward, D.1    Newton, A.2
  • 47
    • 0021930326 scopus 로고
    • DNA gyrase and its complexes with DNA: direct observation by electron microscopy
    • Kirchhausen T., Wang J.C., Harrison S.C. DNA gyrase and its complexes with DNA: direct observation by electron microscopy. Cell 1985, 41:933-943.
    • (1985) Cell , vol.41 , pp. 933-943
    • Kirchhausen, T.1    Wang, J.C.2    Harrison, S.C.3
  • 48
    • 13844275625 scopus 로고    scopus 로고
    • Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit
    • Costenaro L., Grossmann J.G., Ebel C., Maxwell A. Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit. Structure 2005, 13:287-296.
    • (2005) Structure , vol.13 , pp. 287-296
    • Costenaro, L.1    Grossmann, J.G.2    Ebel, C.3    Maxwell, A.4
  • 50
    • 83755172756 scopus 로고    scopus 로고
    • Guiding strand passage: DNA-induced movement of the gyrase C-terminal domains defines an early step in the supercoiling cycle
    • Lanz M.A., Klostermeier D. Guiding strand passage: DNA-induced movement of the gyrase C-terminal domains defines an early step in the supercoiling cycle. Nucleic Acids Res. 2011, 39:9681-9694.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 9681-9694
    • Lanz, M.A.1    Klostermeier, D.2
  • 51
    • 84885630805 scopus 로고    scopus 로고
    • Structural insight into negative DNA supercoiling by DNA gyrase, a bacterial type 2A DNA topoisomerase
    • Papillon J., Menetret J.F., Batisse C., Helye R., Schultz P., Potier N., Lamour V. Structural insight into negative DNA supercoiling by DNA gyrase, a bacterial type 2A DNA topoisomerase. Nucleic Acids Res. 2013, 41:7815-7827.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 7815-7827
    • Papillon, J.1    Menetret, J.F.2    Batisse, C.3    Helye, R.4    Schultz, P.5    Potier, N.6    Lamour, V.7
  • 52
    • 0018039318 scopus 로고
    • DNA-DNA gyrase complex: the wrapping of the DNA duplex outside the enzyme
    • Liu L.F., Wang J.C. DNA-DNA gyrase complex: the wrapping of the DNA duplex outside the enzyme. Cell 1978, 15:979-984.
    • (1978) Cell , vol.15 , pp. 979-984
    • Liu, L.F.1    Wang, J.C.2
  • 53
    • 0029955899 scopus 로고    scopus 로고
    • Conversion of DNA gyrase into a conventional type II topoisomerase
    • Kampranis S.C., Maxwell A. Conversion of DNA gyrase into a conventional type II topoisomerase. Proc. Natl. Acad. Sci. U. S. A. 1996, 93:14416-14421.
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 14416-14421
    • Kampranis, S.C.1    Maxwell, A.2
  • 56
    • 2942528667 scopus 로고    scopus 로고
    • The path of the DNA along the dimer interface of topoisomerase II
    • Roca J. The path of the DNA along the dimer interface of topoisomerase II. J. Biol. Chem. 2004, 279:25783-25788.
    • (2004) J. Biol. Chem. , vol.279 , pp. 25783-25788
    • Roca, J.1
  • 57
    • 69449106505 scopus 로고    scopus 로고
    • The DNA-gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction
    • Gubaev A., Hilbert M., Klostermeier D. The DNA-gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:13278-13283.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 13278-13283
    • Gubaev, A.1    Hilbert, M.2    Klostermeier, D.3
  • 58
    • 84859492187 scopus 로고    scopus 로고
    • Potassium ions are required for nucleotide-induced closure of gyrase N-gate
    • Gubaev A., Klostermeier D. Potassium ions are required for nucleotide-induced closure of gyrase N-gate. J. Biol. Chem. 2012, 287:10916-10921.
    • (2012) J. Biol. Chem. , vol.287 , pp. 10916-10921
    • Gubaev, A.1    Klostermeier, D.2
  • 59
    • 84870584285 scopus 로고    scopus 로고
    • The GyrA-box determines the geometry of DNA bound to gyrase and couples DNA binding to the nucleotide cycle
    • Lanz M.A., Klostermeier D. The GyrA-box determines the geometry of DNA bound to gyrase and couples DNA binding to the nucleotide cycle. Nucleic Acids Res. 2012, 40:10893-10903.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 10893-10903
    • Lanz, M.A.1    Klostermeier, D.2
  • 60
    • 33947147592 scopus 로고    scopus 로고
    • Dissection of the nucleotide cycle of B. subtilis DNA gyrase and its modulation by DNA
    • Gottler T., Klostermeier D. Dissection of the nucleotide cycle of B. subtilis DNA gyrase and its modulation by DNA. J. Mol. Biol. 2007, 367:1392-1404.
    • (2007) J. Mol. Biol. , vol.367 , pp. 1392-1404
    • Gottler, T.1    Klostermeier, D.2
  • 61
    • 0026264213 scopus 로고
    • Sequence specificity of Bacillus subtilis DNA gyrase in vivo
    • Bashkirov V.I., Zvingila D.J. Sequence specificity of Bacillus subtilis DNA gyrase in vivo. Genetica 1991, 85:3-12.
    • (1991) Genetica , vol.85 , pp. 3-12
    • Bashkirov, V.I.1    Zvingila, D.J.2
  • 62
    • 37549023863 scopus 로고    scopus 로고
    • Structural basis for gate-DNA recognition and bending by type IIA topoisomerases
    • Dong K.C., Berger J.M. Structural basis for gate-DNA recognition and bending by type IIA topoisomerases. Nature 2007, 450:1201-1205.
    • (2007) Nature , vol.450 , pp. 1201-1205
    • Dong, K.C.1    Berger, J.M.2
  • 63
    • 0028233250 scopus 로고
    • Evidence for a conformational change in the DNA gyrase-DNA complex from hydroxyl radical footprinting
    • Orphanides G., Maxwell A. Evidence for a conformational change in the DNA gyrase-DNA complex from hydroxyl radical footprinting. Nucleic Acids Res. 1994, 22:1567-1575.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 1567-1575
    • Orphanides, G.1    Maxwell, A.2
  • 65
    • 84862975911 scopus 로고    scopus 로고
    • Conformational changes of DEAD-box helicases monitored by single molecule fluorescence resonance energy transfer
    • Andreou A.Z., Klostermeier D. Conformational changes of DEAD-box helicases monitored by single molecule fluorescence resonance energy transfer. Methods Enzymol. 2012, 511:75-109.
    • (2012) Methods Enzymol. , vol.511 , pp. 75-109
    • Andreou, A.Z.1    Klostermeier, D.2
  • 66
    • 84979155898 scopus 로고    scopus 로고
    • Fluorescence resonance energy transfer as a tool to investigate RNA structure and folding
    • de Gruyter, Berlin, D. Klostermeier, C. Hammann (Eds.)
    • Gubaev A., Klostermeier D. Fluorescence resonance energy transfer as a tool to investigate RNA structure and folding. RNA Structure and Folding 2013, 181-213. de Gruyter, Berlin. D. Klostermeier, C. Hammann (Eds.).
    • (2013) RNA Structure and Folding , pp. 181-213
    • Gubaev, A.1    Klostermeier, D.2
  • 67
    • 0036304446 scopus 로고    scopus 로고
    • The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism
    • Noble C.G., Maxwell A. The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism. J. Mol. Biol. 2002, 318:361-371.
    • (2002) J. Mol. Biol. , vol.318 , pp. 361-371
    • Noble, C.G.1    Maxwell, A.2
  • 69
    • 0030063743 scopus 로고    scopus 로고
    • Energy coupling in Escherichia coli DNA gyrase: the relationship between nucleotide binding, strand passage, and DNA supercoiling
    • Bates A.D., O'Dea M.H., Gellert M. Energy coupling in Escherichia coli DNA gyrase: the relationship between nucleotide binding, strand passage, and DNA supercoiling. Biochemistry 1996, 35:1408-1416.
    • (1996) Biochemistry , vol.35 , pp. 1408-1416
    • Bates, A.D.1    O'Dea, M.H.2    Gellert, M.3
  • 70
    • 0025758726 scopus 로고
    • The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein
    • Reece R.J., Maxwell A. The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein. Nucleic Acids Res. 1991, 19:1399-1405.
    • (1991) Nucleic Acids Res. , vol.19 , pp. 1399-1405
    • Reece, R.J.1    Maxwell, A.2
  • 71
    • 0037870269 scopus 로고    scopus 로고
    • Stabilization of eukaryotic topoisomerase II-DNA cleavage complexes
    • Wilstermann A.M., Osheroff N. Stabilization of eukaryotic topoisomerase II-DNA cleavage complexes. Curr. Top. Med. Chem. 2003, 3:321-338.
    • (2003) Curr. Top. Med. Chem. , vol.3 , pp. 321-338
    • Wilstermann, A.M.1    Osheroff, N.2
  • 72
    • 41449103710 scopus 로고    scopus 로고
    • Using 3'-bridging phosphorothiolates to isolate the forward DNA cleavage reaction of human topoisomerase IIalpha
    • Deweese J.E., Burgin A.B., Osheroff N. Using 3'-bridging phosphorothiolates to isolate the forward DNA cleavage reaction of human topoisomerase IIalpha. Biochemistry 2008, 47:4129-4140.
    • (2008) Biochemistry , vol.47 , pp. 4129-4140
    • Deweese, J.E.1    Burgin, A.B.2    Osheroff, N.3
  • 74
    • 0021715525 scopus 로고
    • The DNA dependence of the ATPase activity of DNA gyrase
    • Maxwell A., Gellert M. The DNA dependence of the ATPase activity of DNA gyrase. J. Biol. Chem. 1984, 259:14472-14480.
    • (1984) J. Biol. Chem. , vol.259 , pp. 14472-14480
    • Maxwell, A.1    Gellert, M.2
  • 75
    • 63349108302 scopus 로고    scopus 로고
    • Topoisomerase II: a fitted mechanism for the chromatin landscape
    • Roca J. Topoisomerase II: a fitted mechanism for the chromatin landscape. Nucleic Acids Res. 2009, 37:721-730.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 721-730
    • Roca, J.1
  • 76
    • 0030444614 scopus 로고    scopus 로고
    • Probing the role of the ATP-operated clamp in the strand-passage reaction of DNA gyrase
    • Tingey A.P., Maxwell A. Probing the role of the ATP-operated clamp in the strand-passage reaction of DNA gyrase. Nucleic Acids Res. 1996, 24:4868-4873.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 4868-4873
    • Tingey, A.P.1    Maxwell, A.2
  • 77
    • 84879905655 scopus 로고    scopus 로고
    • Mapping the spectrum of conformational states of the DNA- and C-gates in Bacillus subtilis gyrase
    • Rudolph M.G., Klostermeier D. Mapping the spectrum of conformational states of the DNA- and C-gates in Bacillus subtilis gyrase. J. Mol. Biol. 2013, 425:2632-2640.
    • (2013) J. Mol. Biol. , vol.425 , pp. 2632-2640
    • Rudolph, M.G.1    Klostermeier, D.2
  • 78
    • 84869097457 scopus 로고    scopus 로고
    • The structure of DNA-bound human topoisomerase II alpha: conformational mechanisms for coordinating inter-subunit interactions with DNA cleavage
    • Wendorff T.J., Schmidt B.H., Heslop P., Austin C.A., Berger J.M. The structure of DNA-bound human topoisomerase II alpha: conformational mechanisms for coordinating inter-subunit interactions with DNA cleavage. J. Mol. Biol. 2012, 424:109-124.
    • (2012) J. Mol. Biol. , vol.424 , pp. 109-124
    • Wendorff, T.J.1    Schmidt, B.H.2    Heslop, P.3    Austin, C.A.4    Berger, J.M.5
  • 79
    • 0032500680 scopus 로고    scopus 로고
    • Hydrolysis of ATP at only one GyrB subunit is sufficient to promote supercoiling by DNA gyrase
    • Kampranis S.C., Maxwell A. Hydrolysis of ATP at only one GyrB subunit is sufficient to promote supercoiling by DNA gyrase. J. Biol. Chem. 1998, 273:26305-26309.
    • (1998) J. Biol. Chem. , vol.273 , pp. 26305-26309
    • Kampranis, S.C.1    Maxwell, A.2
  • 81
    • 0032546589 scopus 로고    scopus 로고
    • Pre-steady-state analysis of ATP hydrolysis by Saccharomyces cerevisiae DNA topoisomerase II. 1. A DNA-dependent burst in ATP hydrolysis
    • Harkins T.T., Lindsley J.E. Pre-steady-state analysis of ATP hydrolysis by Saccharomyces cerevisiae DNA topoisomerase II. 1. A DNA-dependent burst in ATP hydrolysis. Biochemistry 1998, 37:7292-7298.
    • (1998) Biochemistry , vol.37 , pp. 7292-7298
    • Harkins, T.T.1    Lindsley, J.E.2
  • 82
    • 0032546611 scopus 로고    scopus 로고
    • Pre-steady-state analysis of ATP hydrolysis by Saccharomyces cerevisiae DNA topoisomerase II. 2. Kinetic mechanism for the sequential hydrolysis of two ATP
    • Harkins T.T., Lewis T.J., Lindsley J.E. Pre-steady-state analysis of ATP hydrolysis by Saccharomyces cerevisiae DNA topoisomerase II. 2. Kinetic mechanism for the sequential hydrolysis of two ATP. Biochemistry 1998, 37:7299-7312.
    • (1998) Biochemistry , vol.37 , pp. 7299-7312
    • Harkins, T.T.1    Lewis, T.J.2    Lindsley, J.E.3
  • 83
    • 84860751723 scopus 로고    scopus 로고
    • ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA
    • Basu A., Schoeffler A.J., Berger J.M., Bryant Z. ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA. Nat. Struct. Mol. Biol. 2012, 19:538-546.
    • (2012) Nat. Struct. Mol. Biol. , vol.19 , pp. 538-546
    • Basu, A.1    Schoeffler, A.J.2    Berger, J.M.3    Bryant, Z.4
  • 85
    • 34547096540 scopus 로고    scopus 로고
    • DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity
    • Mueller-Planitz F., Herschlag D. DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity. Nucleic Acids Res. 2007, 35:3764-3773.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3764-3773
    • Mueller-Planitz, F.1    Herschlag, D.2
  • 86
    • 34247627894 scopus 로고    scopus 로고
    • Single-molecule measurements of the opening and closing of the DNA gate by eukaryotic topoisomerase II
    • Smiley R.D., Collins T.R., Hammes G.G., Hsieh T.S. Single-molecule measurements of the opening and closing of the DNA gate by eukaryotic topoisomerase II. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:4840-4845.
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 4840-4845
    • Smiley, R.D.1    Collins, T.R.2    Hammes, G.G.3    Hsieh, T.S.4
  • 87
    • 22544467771 scopus 로고    scopus 로고
    • The structural basis for substrate specificity in DNA topoisomerase IV
    • Corbett K.D., Schoeffler A.J., Thomsen N.D., Berger J.M. The structural basis for substrate specificity in DNA topoisomerase IV. J. Mol. Biol. 2005, 351:545-561.
    • (2005) J. Mol. Biol. , vol.351 , pp. 545-561
    • Corbett, K.D.1    Schoeffler, A.J.2    Thomsen, N.D.3    Berger, J.M.4
  • 88
    • 84881660081 scopus 로고    scopus 로고
    • Distinct regions of the Escherichia coli ParC C-terminal domain are required for substrate discrimination by topoisomerase IV
    • Vos S.M., Lee I., Berger J.M. Distinct regions of the Escherichia coli ParC C-terminal domain are required for substrate discrimination by topoisomerase IV. J. Mol. Biol. 2013, 425:3029-3045.
    • (2013) J. Mol. Biol. , vol.425 , pp. 3029-3045
    • Vos, S.M.1    Lee, I.2    Berger, J.M.3
  • 89
    • 84861534674 scopus 로고    scopus 로고
    • Mechanisms for defining supercoiling set point of DNA gyrase orthologs: I. A nonconserved acidic C-terminal tail modulates Escherichia coli gyrase activity
    • Tretter E.M., Berger J.M. Mechanisms for defining supercoiling set point of DNA gyrase orthologs: I. A nonconserved acidic C-terminal tail modulates Escherichia coli gyrase activity. J. Biol. Chem. 2012, 287:18636-18644.
    • (2012) J. Biol. Chem. , vol.287 , pp. 18636-18644
    • Tretter, E.M.1    Berger, J.M.2
  • 90
    • 84861543031 scopus 로고    scopus 로고
    • Mechanisms for defining supercoiling set point of DNA gyrase orthologs: II. The shape of the GyrA subunit C-terminal domain (CTD) is not a sole determinant for controlling supercoiling efficiency
    • Tretter E.M., Berger J.M. Mechanisms for defining supercoiling set point of DNA gyrase orthologs: II. The shape of the GyrA subunit C-terminal domain (CTD) is not a sole determinant for controlling supercoiling efficiency. J. Biol. Chem. 2012, 287:18645-18654.
    • (2012) J. Biol. Chem. , vol.287 , pp. 18645-18654
    • Tretter, E.M.1    Berger, J.M.2
  • 91
    • 0034737716 scopus 로고    scopus 로고
    • Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center
    • Brino L., Urzhumtsev A., Mousli M., Bronner C., Mitschler A., Oudet P., Moras D. Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center. J. Biol. Chem. 2000, 275:9468-9475.
    • (2000) J. Biol. Chem. , vol.275 , pp. 9468-9475
    • Brino, L.1    Urzhumtsev, A.2    Mousli, M.3    Bronner, C.4    Mitschler, A.5    Oudet, P.6    Moras, D.7


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