메뉴 건너뛰기




Volumn 35, Issue 11, 2007, Pages 3764-3773

DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA TOPOISOMERASE (ATP HYDROLYSING); DOUBLE STRANDED DNA; GENOMIC DNA; PLASMID DNA; DNA BINDING PROTEIN;

EID: 34547096540     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm335     Document Type: Article
Times cited : (24)

References (46)
  • 1
    • 0030014783 scopus 로고    scopus 로고
    • DNA topoisomerases
    • Wang,J.C. (1996) DNA topoisomerases. Annu. Rev. Biochem., 65 635-692.
    • (1996) Annu. Rev. Biochem , vol.65 , pp. 635-692
    • Wang, J.C.1
  • 2
    • 2442599792 scopus 로고    scopus 로고
    • Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases
    • Corbett,K.D. and Berger,J.M. (2004) Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annu. Rev. Biophys. Biomol. Struct., 33, 95-118.
    • (2004) Annu. Rev. Biophys. Biomol. Struct , vol.33 , pp. 95-118
    • Corbett, K.D.1    Berger, J.M.2
  • 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. (2005) Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism. Biochem. Soc. Trans., 33, 1465-1470.
    • (2005) Biochem. Soc. Trans , vol.33 , pp. 1465-1470
    • Schoeffler, A.J.1    Berger, J.M.2
  • 4
    • 0027520798 scopus 로고
    • On the coupling between ATP usage and DNA transport by yeast DNA topoisomerase II
    • Lindsley,J.E. and Wang,J.C. (1993) On the coupling between ATP usage and DNA transport by yeast DNA topoisomerase II. J. Biol. Chem., 268, 8096-8104.
    • (1993) J. Biol. Chem , vol.268 , pp. 8096-8104
    • Lindsley, J.E.1    Wang, J.C.2
  • 6
    • 0022431874 scopus 로고
    • Drosophila topoisomerase II double-strand DNA cleavage: Analysis of DNA sequence homology at the cleavage site
    • Sander,M. and Hsieh,T.S. (1985) Drosophila topoisomerase II double-strand DNA cleavage: Analysis of DNA sequence homology at the cleavage site. Nucleic Acids Res., 13, 1057-1072.
    • (1985) Nucleic Acids Res , vol.13 , pp. 1057-1072
    • Sander, M.1    Hsieh, T.S.2
  • 7
    • 0023902435 scopus 로고
    • A consensus sequence for cleavage by vertebrate DNA topoisomerase II
    • Spitzner,J.R. and Muller,M.T. (1988) A consensus sequence for cleavage by vertebrate DNA topoisomerase II. Nucleic Acids Res., 16, 5533-5556.
    • (1988) Nucleic Acids Res , vol.16 , pp. 5533-5556
    • Spitzner, J.R.1    Muller, M.T.2
  • 8
    • 0025056628 scopus 로고
    • Eukaryotic topoisomerase II preferentially cleaves alternating purine-pyrimidine repeats
    • Spitzner,J.R., Chung,I.K. and Muller,M.T. (1990) Eukaryotic topoisomerase II preferentially cleaves alternating purine-pyrimidine repeats. Nucleic Acids Res., 18, 1-11.
    • (1990) Nucleic Acids Res , vol.18 , pp. 1-11
    • Spitzner, J.R.1    Chung, I.K.2    Muller, M.T.3
  • 9
    • 0030448769 scopus 로고    scopus 로고
    • Drug sensitivity and sequence specificity of human recombinant DNA topoisomerases IIalpha (p170) and IIbeta (p180)
    • Cornarotti,M., Tinelli,S., Willmore,E., Zunino,F., Fisher,L.M., Austin,C.A. and Capranico,G. (1996) Drug sensitivity and sequence specificity of human recombinant DNA topoisomerases IIalpha (p170) and IIbeta (p180). Mol. Pharmacol., 50, 1463-1471.
    • (1996) Mol. Pharmacol , vol.50 , pp. 1463-1471
    • Cornarotti, M.1    Tinelli, S.2    Willmore, E.3    Zunino, F.4    Fisher, L.M.5    Austin, C.A.6    Capranico, G.7
  • 10
    • 0026093801 scopus 로고
    • Local base sequence preferences for DNA cleavage by mammalian topoisomerase II in the presence of amsacrine or teniposide
    • Pommier,Y., Capranico,G., Orr,A. and Kohn,K.W. (1991) Local base sequence preferences for DNA cleavage by mammalian topoisomerase II in the presence of amsacrine or teniposide. Nucleic Acids Res., 19 5973-5980.
    • (1991) Nucleic Acids Res , vol.19 , pp. 5973-5980
    • Pommier, Y.1    Capranico, G.2    Orr, A.3    Kohn, K.W.4
  • 11
    • 0025027323 scopus 로고
    • Local sequence requirements for DNA cleavage by mammalian topoisomerase II in the presence of doxorubicin
    • Capranico,G., Kohn,K.W. and Pommier,Y. (1990) Local sequence requirements for DNA cleavage by mammalian topoisomerase II in the presence of doxorubicin. Nucleic Acids Res., 18, 6611-6619.
    • (1990) Nucleic Acids Res , vol.18 , pp. 6611-6619
    • Capranico, G.1    Kohn, K.W.2    Pommier, Y.3
  • 13
    • 0033548660 scopus 로고    scopus 로고
    • Mutation of a conserved serine residue in a quinolone-resistant type II topoisomerase alters the enzyme-DNA and drug interactions
    • Strumberg,D., Nitiss,J.L., Rose,A., Nicklaus,M.C. and Pommier,Y. (1999) Mutation of a conserved serine residue in a quinolone-resistant type II topoisomerase alters the enzyme-DNA and drug interactions. J. Biol. Chem., 274, 7292-7301.
    • (1999) J. Biol. Chem , vol.274 , pp. 7292-7301
    • Strumberg, D.1    Nitiss, J.L.2    Rose, A.3    Nicklaus, M.C.4    Pommier, Y.5
  • 14
    • 0033582466 scopus 로고    scopus 로고
    • In vitro evolution of preferred topoisomerase II DNA cleavage sites
    • Burden,D.A. and Osheroff,N. (1999) In vitro evolution of preferred topoisomerase II DNA cleavage sites. J. Biol. Chem., 274, 5227-5235.
    • (1999) J. Biol. Chem , vol.274 , pp. 5227-5235
    • Burden, D.A.1    Osheroff, N.2
  • 15
    • 0025740443 scopus 로고
    • Nuclear matrix attachment regions and topoisamerase II binding and reaction sites in the vicinity of a chicken DNA replication origin
    • Razin,S.V., Vassetzky,Y.S. and Hancock,R. (1991) Nuclear matrix attachment regions and topoisamerase II binding and reaction sites in the vicinity of a chicken DNA replication origin. Biochem. Biophys. Res. Commun., 177, 265-270.
    • (1991) Biochem. Biophys. Res. Commun , vol.177 , pp. 265-270
    • Razin, S.V.1    Vassetzky, Y.S.2    Hancock, R.3
  • 16
    • 0026526740 scopus 로고
    • In vivo topoisomerase II cleavage of the Drosophila histone and satellite III repeats: DNA sequence and structural characteristics
    • Kas,E. and Laemmli,U.K. (1992) In vivo topoisomerase II cleavage of the Drosophila histone and satellite III repeats: DNA sequence and structural characteristics. EMBO J., 11, 705-716.
    • (1992) EMBO J , vol.11 , pp. 705-716
    • Kas, E.1    Laemmli, U.K.2
  • 17
    • 0030741586 scopus 로고    scopus 로고
    • Distribution of topoisomerase II-mediated cleavage sites and relation to structural and functional landmarks in 830 kb of Drosophila DNA
    • Miassod,R., Razin,S.V. and Hancock,R. (1997) Distribution of topoisomerase II-mediated cleavage sites and relation to structural and functional landmarks in 830 kb of Drosophila DNA. Nucleic Acids Res. 25, 2041-2046.
    • (1997) Nucleic Acids Res , vol.25 , pp. 2041-2046
    • Miassod, R.1    Razin, S.V.2    Hancock, R.3
  • 18
    • 33747743113 scopus 로고    scopus 로고
    • Interdomain communication in DNA topoisomerase II: DNA binding and enzyme activation
    • Mueller-Planitz,F. and Herschlag,D. (2006) Interdomain communication in DNA topoisomerase II: DNA binding and enzyme activation. J. Biol. Chem., 281, 23395-23404.
    • (2006) J. Biol. Chem , vol.281 , pp. 23395-23404
    • Mueller-Planitz, F.1    Herschlag, D.2
  • 19
    • 0026503668 scopus 로고
    • A role for the passage helix in the DNA cleavage reaction of eukaryotic topoisomerase II. A two-site model for enzyme-mediated DNA cleavage
    • Corbett,A.H., Zechiedrich,E.L. and 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. J. Biol. Chem. 267, 683-686.
    • (1992) J. Biol. Chem , vol.267 , pp. 683-686
    • Corbett, A.H.1    Zechiedrich, E.L.2    Osheroff, N.3
  • 20
    • 0033214044 scopus 로고    scopus 로고
    • Molecular analysis of yeast and human type II topoisomerases. Enzyme-DNA and drug interactions
    • Strumberg,D., Nitiss,J.L., Dong,J., Kohn,K.W. and Pommier,Y. (1999) Molecular analysis of yeast and human type II topoisomerases. Enzyme-DNA and drug interactions. J. Biol. Chem., 274, 28246-28255.
    • (1999) J. Biol. Chem , vol.274 , pp. 28246-28255
    • Strumberg, D.1    Nitiss, J.L.2    Dong, J.3    Kohn, K.W.4    Pommier, Y.5
  • 21
    • 0023653150 scopus 로고
    • Calcium-promoted DNA cleavage by eukaryotic topoisomerase II: Trapping the covalent enzyme-DNA complex in an active form
    • Osheroff,N. and Zechiedrich,E.L. (1987) Calcium-promoted DNA cleavage by eukaryotic topoisomerase II: Trapping the covalent enzyme-DNA complex in an active form. Biochemistry, 26, 4303-4309.
    • (1987) Biochemistry , vol.26 , pp. 4303-4309
    • Osheroff, N.1    Zechiedrich, E.L.2
  • 22
    • 0024971102 scopus 로고
    • Single strand DNA cleavage reaction of duplex DNA by Drosophila topoisomerase II
    • Lee,M.P., Sander,M. and Hsieh,T.S. (1989) Single strand DNA cleavage reaction of duplex DNA by Drosophila topoisomerase II. J. Biol. Chem. 264, 13510-13518.
    • (1989) J. Biol. Chem , vol.264 , pp. 13510-13518
    • Lee, M.P.1    Sander, M.2    Hsieh, T.S.3
  • 23
    • 0036720073 scopus 로고    scopus 로고
    • Importance of the fourth alpha-helix within the CAP homology domain of type II topoisomerase for DNA cleavage site recognition and quinolone action
    • Strumberg,D.; Nitiss,J.L., Dong,J., Walker,J., Nicklaus,M.C., Kohn,K.W., Heddle,J.G., Maxwell,A., Seeber,S. et al. (2002) Importance of the fourth alpha-helix within the CAP homology domain of type II topoisomerase for DNA cleavage site recognition and quinolone action. Antimicrob. Agents Chemother., 46, 2735-2746.
    • (2002) Antimicrob. Agents Chemother , vol.46 , pp. 2735-2746
    • Strumberg, D.1    Nitiss, J.L.2    Dong, J.3    Walker, J.4    Nicklaus, M.C.5    Kohn, K.W.6    Heddle, J.G.7    Maxwell, A.8    Seeber, S.9
  • 24
    • 0025119181 scopus 로고
    • Characterization of the interaction between topoisomerase II and DNA by transcriptional footprinting
    • Thomsen,B., Bendixen,C., Lund,K., Andersen,A.H., Sorensen,B.S. and Westergaard,O. (1990) Characterization of the interaction between topoisomerase II and DNA by transcriptional footprinting. J. Mol. Biol., 215, 237-244.
    • (1990) J. Mol. Biol , vol.215 , pp. 237-244
    • Thomsen, B.1    Bendixen, C.2    Lund, K.3    Andersen, A.H.4    Sorensen, B.S.5    Westergaard, O.6
  • 25
    • 0024849694 scopus 로고
    • Nuclease protection by Drosophila DNA topoisomerase II. Enzyme/DNA contacts at the strong topoisomerase II cleavage sites
    • Lee,M.P., Sander,M. and Hsieh,T. (1989) Nuclease protection by Drosophila DNA topoisomerase II. Enzyme/DNA contacts at the strong topoisomerase II cleavage sites. J. Biol. Chem., 264, 21779-21787.
    • (1989) J. Biol. Chem , vol.264 , pp. 21779-21787
    • Lee, M.P.1    Sander, M.2    Hsieh, T.3
  • 26
    • 0030736323 scopus 로고    scopus 로고
    • Protein-DNA recognition complexes: Conservation of structure and binding energy in the transition state
    • Jen-Jacobson,L. (1997) Protein-DNA recognition complexes: Conservation of structure and binding energy in the transition state. Biopolymers 44, 153-180.
    • (1997) Biopolymers , vol.44 , pp. 153-180
    • Jen-Jacobson, L.1
  • 28
    • 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. (1996) Structure and mechanism of DNA topoisomerase II. Nature, 379, 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
  • 29
    • 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. (1999) Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands. Nat. Struct. Biol., 6, 322-326.
    • (1999) Nat. Struct. Biol , vol.6 , pp. 322-326
    • Fass, D.1    Bogden, C.E.2    Berger, J.M.3
  • 30
    • 11244308067 scopus 로고    scopus 로고
    • Structure of the topoisomerase IV C-terminal domain: A broken beta-propeller implies a role as geometry facilitator in catalysis
    • Hsieh,T.J., Farh,L., Huang,W.M. and Chan,N.L. (2004) Structure of the topoisomerase IV C-terminal domain: A broken beta-propeller implies a role as geometry facilitator in catalysis. J. Biol. Chem., 279 55587-55593.
    • (2004) J. Biol. Chem , vol.279 , pp. 55587-55593
    • Hsieh, T.J.1    Farh, L.2    Huang, W.M.3    Chan, N.L.4
  • 31
    • 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. (2004) The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Proc. Natl Acad. Sci. USA, 101, 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
  • 32
    • 0024398661 scopus 로고
    • Tryptic fragments of the Escherichia coli DNA gyrase A protein
    • Reece,R.J. and Maxwell,A. (1989) Tryptic fragments of the Escherichia coli DNA gyrase A protein. J. Biol. Chem., 264, 19648-19653.
    • (1989) J. Biol. Chem , vol.264 , pp. 19648-19653
    • Reece, R.J.1    Maxwell, A.2
  • 33
    • 0025726701 scopus 로고
    • Probing the limits of the DNA breakage-reunion domain of the Escherichia coli DNA gyrase A protein
    • Reece,R.J. and Maxwell,A. (1991) Probing the limits of the DNA breakage-reunion domain of the Escherichia coli DNA gyrase A protein. J. Biol. Chem., 266, 3540-3546.
    • (1991) J. Biol. Chem , vol.266 , pp. 3540-3546
    • Reece, R.J.1    Maxwell, A.2
  • 34
    • 0017968152 scopus 로고
    • Micrococcus luteus DNA gyrase: Active components and a model for its supercoiling of DNA
    • Liu,L.F. and Wang,J.C. (1978) Micrococcus luteus DNA gyrase: Active components and a model for its supercoiling of DNA. Proc. Natl Acad. Sci. USA, 75, 2098-2102.
    • (1978) Proc. Natl Acad. Sci. USA , vol.75 , pp. 2098-2102
    • Liu, L.F.1    Wang, J.C.2
  • 35
    • 0018039318 scopus 로고
    • DNA-DNA gyrase complex: The wrapping of the DNA duplex outside the enzyme
    • Liu,L.F. and Wang,J.C. (1978) DNA-DNA gyrase complex: The wrapping of the DNA duplex outside the enzyme. Cell, 15, 979-984.
    • (1978) Cell , vol.15 , pp. 979-984
    • Liu, L.F.1    Wang, J.C.2
  • 36
    • 33748991182 scopus 로고    scopus 로고
    • Ability of viral topoisomerase II to discern the handedness of supercoiled DNA: Bimodal recognition of DNA geometry by type II enzymes
    • McClendon,A.K., Dickey,J.S. and 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.
    • (2006) Biochemistry , vol.45 , pp. 11674-11680
    • McClendon, A.K.1    Dickey, J.S.2    Osheroff, N.3
  • 37
    • 0037008011 scopus 로고    scopus 로고
    • Multiple conformational changes in enzyme catalysis
    • Hammes,G.G. (2002) Multiple conformational changes in enzyme catalysis. Biochemistry, 41, 8221-8228.
    • (2002) Biochemistry , vol.41 , pp. 8221-8228
    • Hammes, G.G.1
  • 39
    • 84892166712 scopus 로고
    • Einfluss der Configuration auf die Wirkung der Enzyme
    • Fisher,E. (1894) Einfluss der Configuration auf die Wirkung der Enzyme. Ber. Dt. Chem. Ges., 27, 2985-2993.
    • (1894) Ber. Dt. Chem. Ges , vol.27 , pp. 2985-2993
    • Fisher, E.1
  • 40
    • 0001858251 scopus 로고
    • Application of a Theory of Enzyme Specificity to Protein Synthesis
    • Koshland,D.E. (1958) Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc. Natl Acad. Sci. USA, 44, 98-104.
    • (1958) Proc. Natl Acad. Sci. USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 41
    • 0016239830 scopus 로고
    • Enzyme catalysis: Conflicting requirements of substrate access and transition state affinity
    • Wolfenden,R. (1974) Enzyme catalysis: Conflicting requirements of substrate access and transition state affinity. Mol. Cell. Biochem. 3, 207-211.
    • (1974) Mol. Cell. Biochem , vol.3 , pp. 207-211
    • Wolfenden, R.1
  • 43
    • 0024358181 scopus 로고
    • Utilization of binding energy and coupling rules for active transport and other coupled vectorial processes
    • Jencks,W.P. (1989) Utilization of binding energy and coupling rules for active transport and other coupled vectorial processes. Methods Enzymol., 171, 145-164.
    • (1989) Methods Enzymol , vol.171 , pp. 145-164
    • Jencks, W.P.1
  • 44
    • 0023001151 scopus 로고
    • Eukaryotic topoisomerase II. Characterization of enzyme turnover
    • Osheroff,N. (1986) Eukaryotic topoisomerase II. Characterization of enzyme turnover. J. Biol. Chem., 261, 9944-9950.
    • (1986) J. Biol. Chem , vol.261 , pp. 9944-9950
    • Osheroff, N.1
  • 45
    • 0019867850 scopus 로고
    • Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor - operator interaction: Kinetic measurements and conclusions
    • Winter,R.B., Berg,O.G. and von Hippel,P.H. (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor - operator interaction: Kinetic measurements and conclusions. Biochemistry, 20, 6961-6977.
    • (1981) Biochemistry , vol.20 , pp. 6961-6977
    • Winter, R.B.1    Berg, O.G.2    von Hippel, P.H.3
  • 46
    • 0034690257 scopus 로고    scopus 로고
    • Single-molecule analysis of DNA uncoiling by a type II topoisomerase
    • Strick,T.R., Croquette,V. and Bensimon,D. (2000) Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature, 404, 901-904.
    • (2000) Nature , vol.404 , pp. 901-904
    • Strick, T.R.1    Croquette, V.2    Bensimon, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.