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Volumn 367, Issue 5, 2007, Pages 1392-1404

Dissection of the Nucleotide Cycle of B. subtilis DNA Gyrase and its Modulation by DNA

Author keywords

adenine nucleotide binding; DNA binding; DNA gyrase; DNA relaxation; DNA supercoiling

Indexed keywords

ADENOSINE TRIPHOSPHATE; BACTERIAL DNA; DNA TOPOISOMERASE (ATP HYDROLYSING); DNA TOPOISOMERASE (ATP HYDROLYSING) A; DNA TOPOISOMERASE (ATP HYDROLYSING) B; PLASMID DNA; PROTEIN SUBUNIT;

EID: 33947147592     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.01.055     Document Type: Article
Times cited : (22)

References (48)
  • 2
    • 0034923502 scopus 로고    scopus 로고
    • DNA topoisomerases: structure, function, and mechanism
    • Champoux J.J. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70 (2001) 369-413
    • (2001) Annu. Rev. Biochem. , vol.70 , pp. 369-413
    • Champoux, J.J.1
  • 3
    • 28844455588 scopus 로고    scopus 로고
    • Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism
    • Schoeffler A.J., and Berger J.M. Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism. Biochem. Soc. Trans. 33 (2005) 1465-1470
    • (2005) Biochem. Soc. Trans. , vol.33 , pp. 1465-1470
    • Schoeffler, A.J.1    Berger, J.M.2
  • 4
    • 0030045003 scopus 로고    scopus 로고
    • Structure and mechanism of DNA topoisomerase II
    • Berger J.M., Gamblin S.J., Harrison S.C., and Wang J.C. Structure and mechanism of DNA topoisomerase II. Nature 379 (1996) 225-232
    • (1996) Nature , vol.379 , pp. 225-232
    • Berger, J.M.1    Gamblin, S.J.2    Harrison, S.C.3    Wang, J.C.4
  • 5
    • 0032947158 scopus 로고    scopus 로고
    • Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands
    • Fass D., Bogden C.E., and Berger J.M. Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands. Nature Struct. Biol. 6 (1999) 322-326
    • (1999) Nature Struct. Biol. , vol.6 , pp. 322-326
    • Fass, D.1    Bogden, C.E.2    Berger, J.M.3
  • 7
    • 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., and Moras D. Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center. J. Biol. Chem. 275 (2000) 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
  • 8
    • 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., and Dodson G. Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 351 (1991) 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
  • 9
    • 0029961651 scopus 로고    scopus 로고
    • DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism
    • Roca J., Berger J.M., Harrison S.C., and Wang J.C. DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism. Proc. Natl Acad. Sci. USA 93 (1996) 4057-4062
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 4057-4062
    • Roca, J.1    Berger, J.M.2    Harrison, S.C.3    Wang, J.C.4
  • 10
    • 0027520798 scopus 로고
    • On the coupling between ATP usage and DNA transport by yeast DNA topoisomerase II
    • Lindsley J.E., and Wang J.C. On the coupling between ATP usage and DNA transport by yeast DNA topoisomerase II. J. Biol. Chem. 268 (1993) 8096-8104
    • (1993) J. Biol. Chem. , vol.268 , pp. 8096-8104
    • Lindsley, J.E.1    Wang, J.C.2
  • 11
    • 0021099884 scopus 로고
    • DNA topoisomerase II from Drosophila melanogaster. Relaxation of supercoiled DNA
    • Osheroff N., Shelton E.R., and Brutlag D.L. DNA topoisomerase II from Drosophila melanogaster. Relaxation of supercoiled DNA. J. Biol. Chem. 258 (1983) 9536-9543
    • (1983) J. Biol. Chem. , vol.258 , pp. 9536-9543
    • Osheroff, N.1    Shelton, E.R.2    Brutlag, D.L.3
  • 12
    • 0032500680 scopus 로고    scopus 로고
    • Hydrolysis of ATP at only one GyrB subunit is sufficient to promote supercoiling by DNA gyrase
    • Kampranis S.C., and Maxwell A. Hydrolysis of ATP at only one GyrB subunit is sufficient to promote supercoiling by DNA gyrase. J. Biol. Chem. 273 (1998) 26305-26309
    • (1998) J. Biol. Chem. , vol.273 , pp. 26305-26309
    • Kampranis, S.C.1    Maxwell, A.2
  • 13
    • 0021715525 scopus 로고
    • The DNA dependence of the ATPase activity of DNA gyrase
    • Maxwell A., and Gellert M. The DNA dependence of the ATPase activity of DNA gyrase. J. Biol. Chem. 259 (1984) 14472-14480
    • (1984) J. Biol. Chem. , vol.259 , pp. 14472-14480
    • Maxwell, A.1    Gellert, M.2
  • 15
    • 0038128647 scopus 로고    scopus 로고
    • DNA gyrase and DNA topoisomerase of Bacillus subtilis: expression and characterization of recombinant enzymes encoded by the gyrA, gyrB and parC, parE genes
    • Barnes M.H., LaMarr W.A., and Foster K.A. DNA gyrase and DNA topoisomerase of Bacillus subtilis: expression and characterization of recombinant enzymes encoded by the gyrA, gyrB and parC, parE genes. Protein Expr. Purif. 29 (2003) 259-264
    • (2003) Protein Expr. Purif. , vol.29 , pp. 259-264
    • Barnes, M.H.1    LaMarr, W.A.2    Foster, K.A.3
  • 16
    • 0019904477 scopus 로고
    • Bacillus subtilis DNA gyrase: purification of subunits and reconstitution of supercoiling activity
    • Orr E., and Staudenbauer W.L. Bacillus subtilis DNA gyrase: purification of subunits and reconstitution of supercoiling activity. J. Bacteriol. 151 (1982) 524-527
    • (1982) J. Bacteriol. , vol.151 , pp. 524-527
    • Orr, E.1    Staudenbauer, W.L.2
  • 17
    • 0018880839 scopus 로고
    • Bacillus subtilis deoxyribonucleic acid gyrase
    • Sugino A., and Bott K.F. Bacillus subtilis deoxyribonucleic acid gyrase. J. Bacteriol. 141 (1980) 1331-1339
    • (1980) J. Bacteriol. , vol.141 , pp. 1331-1339
    • Sugino, A.1    Bott, K.F.2
  • 18
    • 0017968152 scopus 로고
    • Micrococcus luteus DNA gyrase: active components and a model for its supercoiling of DNA
    • Liu L.F., and Wang J.C. Micrococcus luteus DNA gyrase: active components and a model for its supercoiling of DNA. Proc. Natl Acad. Sci. USA 75 (1978) 2098-2102
    • (1978) Proc. Natl Acad. Sci. USA , vol.75 , pp. 2098-2102
    • Liu, L.F.1    Wang, J.C.2
  • 19
    • 0028844172 scopus 로고
    • Mycobacterial DNA gyrase: enzyme purification and characterization of supercoiling activity
    • Wu L.C., and Shahied S.I. Mycobacterial DNA gyrase: enzyme purification and characterization of supercoiling activity. Arch. Biochem. Biophys. 324 (1995) 123-129
    • (1995) Arch. Biochem. Biophys. , vol.324 , pp. 123-129
    • Wu, L.C.1    Shahied, S.I.2
  • 21
    • 0004952211 scopus 로고
    • Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity
    • Higgins N.P., Peebles C.L., Sugino A., and Cozzarelli N.R. Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity. Proc. Natl Acad. Sci. USA 75 (1978) 1773-1777
    • (1978) Proc. Natl Acad. Sci. USA , vol.75 , pp. 1773-1777
    • Higgins, N.P.1    Peebles, C.L.2    Sugino, A.3    Cozzarelli, N.R.4
  • 22
    • 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., and Maxwell A. Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit. Structure 13 (2005) 287-296
    • (2005) Structure , vol.13 , pp. 287-296
    • Costenaro, L.1    Grossmann, J.G.2    Ebel, C.3    Maxwell, A.4
  • 23
    • 0019322667 scopus 로고
    • Deoxyribonucleic acid gyrase-deoxyribonucleic acid complex containing 140 base pairs of deoxyribonucleic acid and an alpha 2 beta 2 protein core
    • Klevan L., and Wang J.C. Deoxyribonucleic acid gyrase-deoxyribonucleic acid complex containing 140 base pairs of deoxyribonucleic acid and an alpha 2 beta 2 protein core. Biochemistry 19 (1980) 5229-5234
    • (1980) Biochemistry , vol.19 , pp. 5229-5234
    • Klevan, L.1    Wang, J.C.2
  • 24
    • 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., and Maxwell A. The 43-kilodalton N-terminal fragment of the DNA gyrase B protein hydrolyzes ATP and binds coumarin drugs. Biochemistry 32 (1993) 2717-2724
    • (1993) Biochemistry , vol.32 , pp. 2717-2724
    • Ali, J.A.1    Jackson, A.P.2    Howells, A.J.3    Maxwell, A.4
  • 25
    • 0019878168 scopus 로고
    • DNA gyrase: affinity chromatography on novobiocin-Sepharose and catalytic properties
    • Staudenbauer W.L., and Orr E. DNA gyrase: affinity chromatography on novobiocin-Sepharose and catalytic properties. Nucl. Acids Res. 9 (1981) 3589-3603
    • (1981) Nucl. Acids Res. , vol.9 , pp. 3589-3603
    • Staudenbauer, W.L.1    Orr, E.2
  • 26
    • 33747743113 scopus 로고    scopus 로고
    • Interdomain communication in DNA topoisomerase II: DNA binding and enzyme activation
    • Mueller-Planitz F., and Herschlag D. Interdomain communication in DNA topoisomerase II: DNA binding and enzyme activation. J. Biol. Chem. 281 (2007) 23395-23404
    • (2007) J. Biol. Chem. , vol.281 , pp. 23395-23404
    • Mueller-Planitz, F.1    Herschlag, D.2
  • 27
    • 0026264213 scopus 로고
    • Sequence specificity of Bacillus subtilis DNA gyrase in vivo
    • Bashkirov V.I., and Zvingila D.J. Sequence specificity of Bacillus subtilis DNA gyrase in vivo. Genetica 85 (1991) 3-12
    • (1991) Genetica , vol.85 , pp. 3-12
    • Bashkirov, V.I.1    Zvingila, D.J.2
  • 28
    • 0019322527 scopus 로고
    • DNA gyrase subunit stoichiometry and the covalent attachment of subunit A to DNA during DNA cleavage
    • Sugino A., Higgins N.P., and Cozzarelli N.R. DNA gyrase subunit stoichiometry and the covalent attachment of subunit A to DNA during DNA cleavage. Nucl. Acids Res. 8 (1980) 3865-3874
    • (1980) Nucl. Acids Res. , vol.8 , pp. 3865-3874
    • Sugino, A.1    Higgins, N.P.2    Cozzarelli, N.R.3
  • 29
    • 0001534829 scopus 로고
    • Mechanism of action of nalidixic acid: purification of Escherichia coli nalA gene product and its relationship to DNA gyrase and a novel nicking-closing enzyme
    • Sugino A., Peebles C.L., Kreuzer K.N., and Cozzarelli N.R. Mechanism of action of nalidixic acid: purification of Escherichia coli nalA gene product and its relationship to DNA gyrase and a novel nicking-closing enzyme. Proc. Natl Acad. Sci. USA 74 (1977) 4767-4771
    • (1977) Proc. Natl Acad. Sci. USA , vol.74 , pp. 4767-4771
    • Sugino, A.1    Peebles, C.L.2    Kreuzer, K.N.3    Cozzarelli, N.R.4
  • 30
    • 0029166885 scopus 로고
    • Nucleotide binding to the 43-kilodalton N-terminal fragment of the DNA gyrase B protein
    • Ali J.A., Orphanides G., and Maxwell A. Nucleotide binding to the 43-kilodalton N-terminal fragment of the DNA gyrase B protein. Biochemistry 34 (1995) 9801-9808
    • (1995) Biochemistry , vol.34 , pp. 9801-9808
    • Ali, J.A.1    Orphanides, G.2    Maxwell, A.3
  • 31
    • 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., and 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 37 (1998) 7299-7312
    • (1998) Biochemistry , vol.37 , pp. 7299-7312
    • Harkins, T.T.1    Lewis, T.J.2    Lindsley, J.E.3
  • 32
    • 0035958939 scopus 로고    scopus 로고
    • The ATPase reaction cycle of yeast DNA topoisomerase II. Slow rates of ATP resynthesis and P(i) release
    • Baird C.L., Gordon M.S., Andrenyak D.M., Marecek J.F., and Lindsley J.E. The ATPase reaction cycle of yeast DNA topoisomerase II. Slow rates of ATP resynthesis and P(i) release. J. Biol. Chem. 276 (2001) 27893-27898
    • (2001) J. Biol. Chem. , vol.276 , pp. 27893-27898
    • Baird, C.L.1    Gordon, M.S.2    Andrenyak, D.M.3    Marecek, J.F.4    Lindsley, J.E.5
  • 33
    • 0038782340 scopus 로고
    • DNA gyrase: subunit structure and ATPase activity of the purified enzyme
    • Mizuuchi K., O'Dea M.H., and Gellert M. DNA gyrase: subunit structure and ATPase activity of the purified enzyme. Proc. Natl Acad. Sci. USA 75 (1978) 5960-5963
    • (1978) Proc. Natl Acad. Sci. USA , vol.75 , pp. 5960-5963
    • Mizuuchi, K.1    O'Dea, M.H.2    Gellert, M.3
  • 34
    • 0019321370 scopus 로고
    • The intrinsic ATPase of DNA gyrase
    • Sugino A., and Cozzarelli N.R. The intrinsic ATPase of DNA gyrase. J. Biol. Chem. 255 (1980) 6299-6306
    • (1980) J. Biol. Chem. , vol.255 , pp. 6299-6306
    • Sugino, A.1    Cozzarelli, N.R.2
  • 35
    • 4444305118 scopus 로고    scopus 로고
    • Overexpression and purification of Saccharomyces cerevisiae DNA topoisomerase II from yeast
    • Lindsley J.E. Overexpression and purification of Saccharomyces cerevisiae DNA topoisomerase II from yeast. Methods Mol. Biol. 94 (1999) 187-197
    • (1999) Methods Mol. Biol. , vol.94 , pp. 187-197
    • Lindsley, J.E.1
  • 36
    • 0026806953 scopus 로고
    • Slow interaction of 5′-adenylyl-beta,gamma-imidodiphosphate with Escherichia coli DNA gyrase. Evidence for cooperativity in nucleotide binding
    • Tamura J.K., Bates A.D., and Gellert M. Slow interaction of 5′-adenylyl-beta,gamma-imidodiphosphate with Escherichia coli DNA gyrase. Evidence for cooperativity in nucleotide binding. J. Biol. Chem. 267 (1992) 9122-9214
    • (1992) J. Biol. Chem. , vol.267 , pp. 9122-9214
    • Tamura, J.K.1    Bates, A.D.2    Gellert, M.3
  • 37
    • 0033985080 scopus 로고    scopus 로고
    • GHKL, an emergent ATPase/kinase superfamily
    • Dutta R., and Inouye M. GHKL, an emergent ATPase/kinase superfamily. Trends Biochem. Sci. 25 (2000) 24-28
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 24-28
    • Dutta, R.1    Inouye, M.2
  • 38
    • 0034602451 scopus 로고    scopus 로고
    • C-terminal regions of Hsp90 are important for trapping the nucleotide during the ATPase cycle
    • Weikl T., Muschler P., Richter K., Veit T., Reinstein J., and Buchner J. C-terminal regions of Hsp90 are important for trapping the nucleotide during the ATPase cycle. J. Mol. Biol. 303 (2000) 583-592
    • (2000) J. Mol. Biol. , vol.303 , pp. 583-592
    • Weikl, T.1    Muschler, P.2    Richter, K.3    Veit, T.4    Reinstein, J.5    Buchner, J.6
  • 39
    • 7944225978 scopus 로고    scopus 로고
    • Independent ATPase activity of Hsp90 subunits creates a flexible assembly platform
    • McLaughlin S.H., Ventouras L.A., Lobbezoo B., and Jackson S.E. Independent ATPase activity of Hsp90 subunits creates a flexible assembly platform. J. Mol. Biol. 344 (2004) 813-826
    • (2004) J. Mol. Biol. , vol.344 , pp. 813-826
    • McLaughlin, S.H.1    Ventouras, L.A.2    Lobbezoo, B.3    Jackson, S.E.4
  • 40
    • 0033515522 scopus 로고    scopus 로고
    • Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repair
    • Ban C., Junop M., and Yang W. Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repair. Cell 97 (1999) 85-97
    • (1999) Cell , vol.97 , pp. 85-97
    • Ban, C.1    Junop, M.2    Yang, W.3
  • 41
    • 33644847122 scopus 로고    scopus 로고
    • Characterization of a unique type IA topoisomerase in Bacillus cereus
    • Li Z., Hiasa H., and Digate R. Characterization of a unique type IA topoisomerase in Bacillus cereus. Mol. Microbiol. 60 (2006) 140-151
    • (2006) Mol. Microbiol. , vol.60 , pp. 140-151
    • Li, Z.1    Hiasa, H.2    Digate, R.3
  • 42
    • 2442611949 scopus 로고    scopus 로고
    • The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold
    • Corbett K.D., Shultzaberger R.K., and Berger J.M. The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Proc. Natl Acad. Sci. USA 101 (2004) 7293-7298
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 7293-7298
    • Corbett, K.D.1    Shultzaberger, R.K.2    Berger, J.M.3
  • 43
    • 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., and Verdine G.L. A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. J. Biol. Chem. 280 (2005) 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
  • 44
    • 0030731108 scopus 로고    scopus 로고
    • The complete genome sequence of the Gram-positive bacterium Bacillus subtilis
    • Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., et al. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390 (1997) 249-256
    • (1997) Nature , vol.390 , pp. 249-256
    • Kunst, F.1    Ogasawara, N.2    Moszer, I.3    Albertini, A.M.4    Alloni, G.5    Azevedo, V.6
  • 45
    • 0022423296 scopus 로고
    • Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. III. Nucleotide sequence of some 10,000 base pairs in the origin region
    • Moriya S., Ogasawara N., and Yoshikawa H. Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. III. Nucleotide sequence of some 10,000 base pairs in the origin region. Nucl. Acids Res. 13 (1985) 2251-2265
    • (1985) Nucl. Acids Res. , vol.13 , pp. 2251-2265
    • Moriya, S.1    Ogasawara, N.2    Yoshikawa, H.3
  • 46
    • 0008236102 scopus 로고
    • Adenosin-5′diphosphat und Adenosin-5′monophosphat
    • Bergmeyer H.U. (Ed), Verlag Chemie, Weinheim
    • Adam H. Adenosin-5′diphosphat und Adenosin-5′monophosphat. In: Bergmeyer H.U. (Ed). Methoden der Enzymatischen Analyse (1962), Verlag Chemie, Weinheim 573-577
    • (1962) Methoden der Enzymatischen Analyse , pp. 573-577
    • Adam, H.1
  • 48
    • 0020674810 scopus 로고
    • New ribose-modified fluorescent analogs of adenine and guanine nucleotides available as substrates for various enzymes
    • Hiratsuka T. New ribose-modified fluorescent analogs of adenine and guanine nucleotides available as substrates for various enzymes. Biochim. Biophys. Acta 742 (1983) 496-508
    • (1983) Biochim. Biophys. Acta , vol.742 , pp. 496-508
    • Hiratsuka, T.1


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