메뉴 건너뛰기




Volumn 108, Issue 17, 2011, Pages 6939-6944

Crystal structure of a covalent intermediate in DNA cleavage and rejoining by Escherichia coli DNA topoisomerase

Author keywords

Cytosine recognition; DNA relaxation; Protein DNA complex; TopA

Indexed keywords

CYTOSINE; DNA TOPOISOMERASE; OLIGONUCLEOTIDE;

EID: 79955566853     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1100300108     Document Type: Article
Times cited : (59)

References (45)
  • 1
    • 50649101663 scopus 로고    scopus 로고
    • DNA topoisomerases: Harnessing and constraining energy to govern chromosome topology
    • Schoeffler AJ, Berger JM (2008) DNA topoisomerases: Harnessing and constraining energy to govern chromosome topology. Q Rev Biophys 41:41-101.
    • (2008) Q Rev Biophys , vol.41 , pp. 41-101
    • Schoeffler, A.J.1    Berger, J.M.2
  • 2
    • 0036085460 scopus 로고    scopus 로고
    • Cellular roles of DNA topoisomerases: A molecular perspective
    • Wang JC (2002) Cellular roles of DNA topoisomerases: A molecular perspective. Nat Rev Mol Cell Biol 3:430-440.
    • (2002) Nat Rev Mol Cell Biol , vol.3 , pp. 430-440
    • Wang, J.C.1
  • 3
    • 64649090292 scopus 로고    scopus 로고
    • Targeting DNA topoisomerase II in cancer chemotherapy
    • Nitiss JL (2009) Targeting DNA topoisomerase II in cancer chemotherapy. Nat Rev Cancer 9:338-350.
    • (2009) Nat Rev Cancer , vol.9 , pp. 338-350
    • Nitiss, J.L.1
  • 4
    • 77954187741 scopus 로고    scopus 로고
    • DNA topoisomerases and their poisoning by anticancer and antibacterial drugs
    • Pommier Y, Leo E, Zhang H, Marchand C (2010) DNA topoisomerases and their poisoning by anticancer and antibacterial drugs. Chem Biol 17:421-433.
    • (2010) Chem Biol , vol.17 , pp. 421-433
    • Pommier, Y.1    Leo, E.2    Zhang, H.3    Marchand, C.4
  • 5
    • 54849420897 scopus 로고    scopus 로고
    • Recent advances in bacterial topoisomerase inhibitors
    • Bradbury BJ, Pucci MJ (2008) Recent advances in bacterial topoisomerase inhibitors. Curr Opin Pharmacol 8:574-581.
    • (2008) Curr Opin Pharmacol , vol.8 , pp. 574-581
    • Bradbury, B.J.1    Pucci, M.J.2
  • 6
    • 63349102030 scopus 로고    scopus 로고
    • Phylogenomics of DNA topoisomerases: Their origin and putative roles in the emergence of modern organisms
    • Forterre P, Gadelle D (2009) Phylogenomics of DNA topoisomerases: Their origin and putative roles in the emergence of modern organisms. Nucleic Acids Res 37:679-692.
    • (2009) Nucleic Acids Res , vol.37 , pp. 679-692
    • Forterre, P.1    Gadelle, D.2
  • 8
    • 58149083577 scopus 로고    scopus 로고
    • Asp-to-Asn substitution at the first position of the DxD TOPRIM motif of recombinant bacterial topoisomerase I is extremely lethal to E. coli
    • Cheng B, et al. (2009) Asp-to-Asn substitution at the first position of the DxD TOPRIM motif of recombinant bacterial topoisomerase I is extremely lethal to E. coli. J Mol Biol 385:558-567.
    • (2009) J Mol Biol , vol.385 , pp. 558-567
    • Cheng, B.1
  • 9
    • 67749103597 scopus 로고    scopus 로고
    • Hydroxyl radicals are involved in cell killing by the bacterial topoisomerase I cleavage complex
    • Liu IF, Annamalai T, Sutherland JH, Tse-Dinh YC (2009) Hydroxyl radicals are involved in cell killing by the bacterial topoisomerase I cleavage complex. J Bacteriol 191:5315-5319.
    • (2009) J Bacteriol , vol.191 , pp. 5315-5319
    • Liu, I.F.1    Annamalai, T.2    Sutherland, J.H.3    Tse-Dinh, Y.C.4
  • 10
    • 63349088873 scopus 로고    scopus 로고
    • Bacterial topoisomerase I as a target for discovery of antibacterial compounds
    • Tse-Dinh YC (2009) Bacterial topoisomerase I as a target for discovery of antibacterial compounds. Nucleic Acids Res 37:731-737.
    • (2009) Nucleic Acids Res , vol.37 , pp. 731-737
    • Tse-Dinh, Y.C.1
  • 11
    • 77956832926 scopus 로고    scopus 로고
    • The dilemma of multidrug-resistant gram-negative bacteria
    • Engel LS (2010) The dilemma of multidrug-resistant gram-negative bacteria. Am J Med Sci 340:232-237.
    • (2010) Am J Med Sci , vol.340 , pp. 232-237
    • Engel, L.S.1
  • 12
    • 77952298917 scopus 로고    scopus 로고
    • Hospital-acquired infections due to gram-negative bacteria
    • Peleg AY, Hooper DC (2010) Hospital-acquired infections due to gram-negative bacteria. N Engl J Med 362:1804-1813.
    • (2010) N Engl J Med , vol.362 , pp. 1804-1813
    • Peleg, A.Y.1    Hooper, D.C.2
  • 13
    • 77956095797 scopus 로고    scopus 로고
    • Genome-wide analysis of divergence of antibiotic resistance determinants in closely related isolates of Acinetobacter baumannii
    • Adams MD, Chan ER, Molyneaux ND, Bonomo RA (2010) Genome-wide analysis of divergence of antibiotic resistance determinants in closely related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother 54:3569-3577.
    • (2010) Antimicrob Agents Chemother , vol.54 , pp. 3569-3577
    • Adams, M.D.1    Chan, E.R.2    Molyneaux, N.D.3    Bonomo, R.A.4
  • 14
    • 77953208357 scopus 로고    scopus 로고
    • Up against the wall
    • Torres C (2010) Up against the wall. Nat Med 16:628-631.
    • (2010) Nat Med , vol.16 , pp. 628-631
    • Torres, C.1
  • 15
    • 78349254945 scopus 로고    scopus 로고
    • New delhi metallo-beta-lactamase (NDM-1): Towards a new pandemia?
    • Rolain JM, Parola P, Cornaglia G (2010) New delhi metallo-beta-lactamase (NDM-1): Towards a new pandemia? Clin Microbiol Infec 16:1699-1701.
    • (2010) Clin Microbiol Infec , vol.16 , pp. 1699-1701
    • Rolain, J.M.1    Parola, P.2    Cornaglia, G.3
  • 16
    • 77957770819 scopus 로고    scopus 로고
    • Alarming beta-lactamase-mediated resistance in multidrug-resistant enterobacteriaceae
    • Bush K (2010) Alarming beta-lactamase-mediated resistance in multidrug-resistant enterobacteriaceae. Curr Opin Microbiol 13:558-564.
    • (2010) Curr Opin Microbiol , vol.13 , pp. 558-564
    • Bush, K.1
  • 17
  • 18
    • 0032489634 scopus 로고    scopus 로고
    • Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA
    • DOI 10.1126/science.279.5356.1504
    • Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG (1998) Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 279:1504-1513. (Pubitemid 28217069)
    • (1998) Science , vol.279 , Issue.5356 , pp. 1504-1513
    • Redinbo, M.R.1    Stewart, L.2    Kuhn, P.3    Champoux, J.J.4    Hol, W.G.J.5
  • 19
    • 0028115776 scopus 로고
    • Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I
    • DOI 10.1038/367138a0
    • Lima CD, Wang JC, Mondragon A (1994) Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I. Nature 367:138-146. (Pubitemid 24031694)
    • (1994) Nature , vol.367 , Issue.6459 , pp. 138-146
    • Lima, C.D.1    Wang, J.C.2    Mondragon, A.3
  • 22
    • 0035963340 scopus 로고    scopus 로고
    • Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule
    • DOI 10.1038/35082615
    • Changela A, DiGate RJ, Mondragon A (2001) Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Nature 411:1077-1081. (Pubitemid 32612335)
    • (2001) Nature , vol.411 , Issue.6841 , pp. 1077-1081
    • Changela, A.1    DiGate, R.J.2    Mondragon, A.3
  • 23
    • 0032502767 scopus 로고    scopus 로고
    • Site-directed mutagenesis of conserved aspartates, glutamates and arginines in the active site region of Escherichia coli DNA topoisomerase I
    • DOI 10.1074/jbc.273.15.8783
    • Zhu CX, Roche CJ, Papanicolaou N, DiPietrantonio A, Tse-Dinh YC (1998) Site-directed mutagenesis of conserved aspartates, glutamates and arginines in the active site region of Escherichia coli DNA topoisomerase I. J Biol Chem 273:8783-8789. (Pubitemid 28176157)
    • (1998) Journal of Biological Chemistry , vol.273 , Issue.15 , pp. 8783-8789
    • Zhu, C.-X.1    Roche, C.J.2    Papanicolaou, N.3    DiPietrantonio, A.4    Tse-Dinh, Y.-C.5
  • 24
    • 0032513296 scopus 로고    scopus 로고
    • Identification of active site residues in Escherichia coli DNA topoisomerase I
    • Chen SJ, Wang JC (1998) Identification of active site residues in Escherichia coli DNA topoisomerase I. J Biol Chem 273:6050-6056.
    • (1998) J Biol Chem , vol.273 , pp. 6050-6056
    • Chen, S.J.1    Wang, J.C.2
  • 25
    • 4544384634 scopus 로고    scopus 로고
    • Site-directed mutagenesis of residues involved in G strand DNA binding by Escherichia coli DNA topoisomerase I
    • DOI 10.1074/jbc.M405891200
    • Cheng B, Feng J, Mulay V, Gadgil S, Tse-Dinh YC (2004) Site-directed mutagenesis of residues involved in G strand DNA binding by Escherichia coli DNA topoisomerase I. J Biol Chem 279:39207-39213. (Pubitemid 39258181)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.38 , pp. 39207-39213
    • Cheng, B.1    Feng, J.2    Mulay, V.3    Gadgil, S.4    Tse-Dinh, Y.-C.5
  • 26
    • 34247481823 scopus 로고    scopus 로고
    • Type IA topoisomerases: A simple puzzle?
    • Viard T, de la Tour CB (2007) Type IA topoisomerases: A simple puzzle? Biochimie 89:456-467.
    • (2007) Biochimie , vol.89 , pp. 456-467
    • Viard, T.1    De La Tour, C.B.2
  • 27
    • 0019332581 scopus 로고
    • Covalent bonds between protein and DNA. Formation of phosphotyrosine linkage between certain DNA topoisomerases and DNA
    • Tse YC, Kirkegaard K, Wang JC (1980) Covalent bonds between protein and DNA. Formation of phosphotyrosine linkage between certain DNA topoisomerases and DNA. J Biol Chem 255:5560-5565.
    • (1980) J Biol Chem , vol.255 , pp. 5560-5565
    • Tse, Y.C.1    Kirkegaard, K.2    Wang, J.C.3
  • 28
    • 0020262662 scopus 로고
    • Escherichia coli type-1 topoisomerases: Identification, mechanism, and role in recombination
    • Dean F, et al. (1983) Escherichia coli type-1 topoisomerases: Identification, mechanism, and role in recombination. Cold Spring Harb Sym Quant Biol 47(Pt 2):769-777.
    • (1983) Cold Spring Harb Sym Quant Biol , vol.47 , Issue.PART 2 , pp. 769-777
    • Dean, F.1
  • 29
    • 0037066771 scopus 로고    scopus 로고
    • Biochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis
    • DOI 10.1074/jbc.M112019200
    • Perry K, Mondragon A (2002) Biochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis. J Biol Chem 277:13237-13245. (Pubitemid 34952695)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.15 , pp. 13237-13245
    • Perry, K.1    Mondragon, A.2
  • 30
    • 0034008773 scopus 로고    scopus 로고
    • The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change
    • Zhu CX, Tse-Dinh YC (2000) The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change. J Biol Chem 275:5318-5322.
    • (2000) J Biol Chem , vol.275 , pp. 5318-5322
    • Zhu, C.X.1    Tse-Dinh, Y.C.2
  • 31
    • 37549023863 scopus 로고    scopus 로고
    • Structural basis for gate-DNA recognition and bending by type IIA topoisomerases
    • Dong KC, Berger JM (2007) Structural basis for gate-DNA recognition and bending by type IIA topoisomerases. Nature 450:1201-1205.
    • (2007) Nature , vol.450 , pp. 1201-1205
    • Dong, K.C.1    Berger, J.M.2
  • 32
    • 77953229439 scopus 로고    scopus 로고
    • A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases
    • Schmidt BH, Burgin AB, Deweese JE, Osheroff N, Berger JM (2010) A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases. Nature 465:641-644.
    • (2010) Nature , vol.465 , pp. 641-644
    • Schmidt, B.H.1    Burgin, A.B.2    Deweese, J.E.3    Osheroff, N.4    Berger, J.M.5
  • 33
    • 0032489675 scopus 로고    scopus 로고
    • A model for the mechanism of human topoisomerase I
    • DOI 10.1126/science.279.5356.1534
    • Stewart L, Redinbo MR, Qiu X, Hol WG, Champoux JJ (1998) A model for the mechanism of human topoisomerase I. Science 279:1534-1541. (Pubitemid 28217077)
    • (1998) Science , vol.279 , Issue.5356 , pp. 1534-1541
    • Stewart, L.1    Redinbo, M.R.2    Qiu, X.3    Hol, W.G.J.4    Champoux, J.J.5
  • 34
    • 0037126054 scopus 로고    scopus 로고
    • The mechanism of type IA topoisomerases
    • Dekker NH, et al. (2002) The mechanism of type IA topoisomerases. Proc Natl Acad Sci USA 99:12126-12131.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 12126-12131
    • Dekker, N.H.1
  • 36
    • 0031006668 scopus 로고    scopus 로고
    • Vaccinia DNA topoisomerase I: Evidence supporting a free rotation mechanism for DNA supercoil relaxation
    • DOI 10.1021/bi962880t
    • Stivers JT, Harris TK, Mildvan AS (1997) Vaccinia DNA topoisomerase I: Evidence supporting a free rotation mechanism for DNA supercoil relaxation. Biochemistry 36:5212-5222. (Pubitemid 27199738)
    • (1997) Biochemistry , vol.36 , Issue.17 , pp. 5212-5222
    • Stivers, J.T.1    Harris, T.K.2    Mildvan, A.S.3
  • 37
    • 15844383117 scopus 로고    scopus 로고
    • Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB
    • DOI 10.1038/nature03395
    • Koster DA, Croquette V, Dekker C, Shuman S, Dekker NH (2005) Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature 434:671-674. (Pubitemid 40488562)
    • (2005) Nature , vol.434 , Issue.7033 , pp. 671-674
    • Koster, D.A.1    Croquette, V.2    Dekker, C.3    Shuman, S.4    Dekker, N.H.5
  • 38
    • 33947322802 scopus 로고    scopus 로고
    • Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate
    • DOI 10.1016/j.jmb.2007.01.065, PII S0022283607001295
    • Changela A, DiGate RJ, Mondragon A (2007) Structural studies of E. coli topoisomerase III-DNA complexes reveal a novel type IA topoisomerase-DNA conformational intermediate. J Mol Biol 368:105-118. (Pubitemid 46441213)
    • (2007) Journal of Molecular Biology , vol.368 , Issue.1 , pp. 105-118
    • Changela, A.1    DiGate, R.J.2    Mondragon, A.3
  • 39
    • 67650682519 scopus 로고    scopus 로고
    • DNA topoisomerase I inhibitors: Chemistry, biology, and interfacial inhibition
    • Pommier Y (2009) DNA topoisomerase I inhibitors: Chemistry, biology, and interfacial inhibition. Chem Rev 109:2894-2902.
    • (2009) Chem Rev , vol.109 , pp. 2894-2902
    • Pommier, Y.1
  • 40
    • 49249107295 scopus 로고    scopus 로고
    • 2+ binding and DNA religation by bacterial topoisomerase I via introduction of an additional positive charge into the active site region
    • 2+ binding and DNA religation by bacterial topoisomerase I via introduction of an additional positive charge into the active site region. Nucleic Acids Res 36:4788-4796.
    • (2008) Nucleic Acids Res , vol.36 , pp. 4788-4796
    • Sorokin, E.P.1
  • 41
    • 33745933955 scopus 로고    scopus 로고
    • HKL-3000: The integration of data reduction and structure solution - From diffraction images to an initial model in minutes
    • DOI 10.1107/S0907444906019949
    • Minor W, Cymborowski M, Otwinowski Z, Chruszcz M (2006) HKL-3000: The integration of data reduction and structure solution - from diffraction images to an initial model in minutes. Acta Crystallogr D 62:859-866. (Pubitemid 44125661)
    • (2006) Acta Crystallographica Section D: Biological Crystallography , vol.62 , Issue.8 , pp. 859-866
    • Minor, W.1    Cymborowski, M.2    Otwinowski, Z.3    Chruszcz, M.4
  • 42
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project N4
    • Collaborative Computational Project N4 (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D 50:760-763.
    • (1994) Acta Crystallogr D , vol.50 , pp. 760-763
  • 43
    • 3543012707 scopus 로고    scopus 로고
    • Crystallography & NMR system: A new software suite for macromolecular structure determination
    • Brunger AT, et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D 54:905-921.
    • (1998) Acta Crystallogr D , vol.54 , pp. 905-921
    • Brunger, A.T.1
  • 44
    • 3342973624 scopus 로고    scopus 로고
    • Overexpression and purification of bacterial DNA topoisomerase I
    • Zhu CX, Tse-Dinh YC (1999) Overexpression and purification of bacterial DNA topoisomerase I. Methods Mol Biol 94:145-151.
    • (1999) Methods Mol Biol , vol.94 , pp. 145-151
    • Zhu, C.X.1    Tse-Dinh, Y.C.2
  • 45
    • 1542275519 scopus 로고    scopus 로고
    • Flexibility at Gly-194 Is Required for DNA Cleavage and Relaxation Activity of Escherichia coli DNA Topoisomerase I
    • DOI 10.1074/jbc.M312095200
    • Cheng B, Feng J, Gadgil S, Tse-Dinh YC (2004) Flexibility at Gly-194 is required for DNA cleavage and relaxation activity of Escherichia coli DNA topoisomerase I. J Biol Chem 279:8648-8654. (Pubitemid 38295920)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.10 , pp. 8648-8654
    • Cheng, B.1    Feng, J.2    Gadgil, S.3    Tse-Dinh, Y.-C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.