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Volumn 289, Issue 5479, 2000, Pages 619-625

A structural model of transcription elongation

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; DOUBLE STRANDED DNA; NUCLEIC ACID; RIFAMPICIN; RNA POLYMERASE;

EID: 0034725870     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.289.5479.619     Document Type: Article
Times cited : (340)

References (59)
  • 1
    • 0344271983 scopus 로고
    • D. Sweetser, M. Nonet, R. A. Young, Proc. Natl. Acad. Sci. U.S.A. 84, 1192 (1987); R. S. Jokerst, J. R. Weeks, W. A. Zehring, A. L. Greenleaf, Mol. Gen. Genet. 215, 266 (1989); J. Archambault and J. D. Friesen, Microbiol. Rev. 57, 703 (1993).
    • (1987) Proc. Natl. Acad. Sci. U.S.A. , vol.84 , pp. 1192
    • Sweetser, D.1    Nonet, M.2    Young, R.A.3
  • 2
    • 0024557468 scopus 로고
    • D. Sweetser, M. Nonet, R. A. Young, Proc. Natl. Acad. Sci. U.S.A. 84, 1192 (1987); R. S. Jokerst, J. R. Weeks, W. A. Zehring, A. L. Greenleaf, Mol. Gen. Genet. 215, 266 (1989); J. Archambault and J. D. Friesen, Microbiol. Rev. 57, 703 (1993).
    • (1989) Mol. Gen. Genet. , vol.215 , pp. 266
    • Jokerst, R.S.1    Weeks, J.R.2    Zehring, W.A.3    Greenleaf, A.L.4
  • 3
    • 0027306799 scopus 로고
    • D. Sweetser, M. Nonet, R. A. Young, Proc. Natl. Acad. Sci. U.S.A. 84, 1192 (1987); R. S. Jokerst, J. R. Weeks, W. A. Zehring, A. L. Greenleaf, Mol. Gen. Genet. 215, 266 (1989); J. Archambault and J. D. Friesen, Microbiol. Rev. 57, 703 (1993).
    • (1993) Microbiol. Rev. , vol.57 , pp. 703
    • Archambault, J.1    Friesen, J.D.2
  • 4
    • 0001323636 scopus 로고
    • F. C. Neidhardt, Ed. American Society for Microbiology, Washington, DC
    • T. D. Yager and P. von Hippel, in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, F. C. Neidhardt, Ed. (American Society for Microbiology, Washington, DC, 1987), p. 1241; M. J. Chamberlin, Harvey Lect. 88, 1 (1993); J. Gelles and R. Landick, Cell 93, 13 (1998); R. A. Mooney, I. Artsimovitch, R. Landick, J. Bacteriol. 180, 3265 (1998).
    • (1987) Escherichia Coli and Salmonella Typhimurium: Cellular and Molecular Biology , pp. 1241
    • Yager, T.D.1    Von Hippel, P.2
  • 5
    • 0027106595 scopus 로고
    • T. D. Yager and P. von Hippel, in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, F. C. Neidhardt, Ed. (American Society for Microbiology, Washington, DC, 1987), p. 1241; M. J. Chamberlin, Harvey Lect. 88, 1 (1993); J. Gelles and R. Landick, Cell 93, 13 (1998); R. A. Mooney, I. Artsimovitch, R. Landick, J. Bacteriol. 180, 3265 (1998).
    • (1993) Harvey Lect. , vol.88 , pp. 1
    • Chamberlin, M.J.1
  • 6
    • 0032478549 scopus 로고    scopus 로고
    • T. D. Yager and P. von Hippel, in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, F. C. Neidhardt, Ed. (American Society for Microbiology, Washington, DC, 1987), p. 1241; M. J. Chamberlin, Harvey Lect. 88, 1 (1993); J. Gelles and R. Landick, Cell 93, 13 (1998); R. A. Mooney, I. Artsimovitch, R. Landick, J. Bacteriol. 180, 3265 (1998).
    • (1998) Cell , vol.93 , pp. 13
    • Gelles, J.1    Landick, R.2
  • 7
    • 0031801743 scopus 로고    scopus 로고
    • T. D. Yager and P. von Hippel, in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, F. C. Neidhardt, Ed. (American Society for Microbiology, Washington, DC, 1987), p. 1241; M. J. Chamberlin, Harvey Lect. 88, 1 (1993); J. Gelles and R. Landick, Cell 93, 13 (1998); R. A. Mooney, I. Artsimovitch, R. Landick, J. Bacteriol. 180, 3265 (1998).
    • (1998) J. Bacteriol. , vol.180 , pp. 3265
    • Mooney, R.A.1    Artsimovitch, I.2    Landick, R.3
  • 11
    • 0033578701 scopus 로고    scopus 로고
    • G. Zhang et al., Cell 98, 811 (1999).
    • (1999) Cell , vol.98 , pp. 811
    • Zhang, G.1
  • 12
    • 0343842821 scopus 로고    scopus 로고
    • See supplementary material at Science Online at www.sciencemag.org/feature/data/1051897.shl..
    • Science
  • 15
    • 0018867360 scopus 로고
    • U. Siebenlist, R. B. Simpson, W. Gilbert, Cell 20, 269 (1980); K. Kirkegaard, H. Buc, A. Spassky, J. C. Wang, Proc. Narl. Acad. Sci. U.S.A. 80, 2544 (1983); J. Mecsas, D. W. Cowing, C. A. Gross, J. Mol. Biol. 220, 585 (1991);
    • (1980) Cell , vol.20 , pp. 269
    • Siebenlist, U.1    Simpson, R.B.2    Gilbert, W.3
  • 17
    • 0025785249 scopus 로고
    • U. Siebenlist, R. B. Simpson, W. Gilbert, Cell 20, 269 (1980); K. Kirkegaard, H. Buc, A. Spassky, J. C. Wang, Proc. Narl. Acad. Sci. U.S.A. 80, 2544 (1983); J. Mecsas, D. W. Cowing, C. A. Gross, J. Mol. Biol. 220, 585 (1991);
    • (1991) J. Mol. Biol. , vol.220 , pp. 585
    • Mecsas, J.1    Cowing, D.W.2    Gross, C.A.3
  • 22
    • 0030584091 scopus 로고    scopus 로고
    • T. C. Reeder and D. K. Hawley, Cell 87, 767 (1996); N. Komissarova and M. Kashlev, J. Biol. Chem. 272, 15329 (1997).
    • (1996) Cell , vol.87 , pp. 767
    • Reeder, T.C.1    Hawley, D.K.2
  • 26
    • 0032518398 scopus 로고    scopus 로고
    • S. Doublie, S. Tabor, A. M. Long, C. C. Richardson, T. Ellenberger, Nature 391, 251 (1998); J. R. Kiefer, C. Mao, J. C. Braman, L. S. Beese, Nature 391, 304 (1998); G. M. T. Cheetham, D. Jeruzalmi, T. A. Steitz, Nature 399, 80 (1999).
    • (1998) Nature , vol.391 , pp. 251
    • Doublie, S.1    Tabor, S.2    Long, A.M.3    Richardson, C.C.4    Ellenberger, T.5
  • 27
    • 0032518524 scopus 로고    scopus 로고
    • S. Doublie, S. Tabor, A. M. Long, C. C. Richardson, T. Ellenberger, Nature 391, 251 (1998); J. R. Kiefer, C. Mao, J. C. Braman, L. S. Beese, Nature 391, 304 (1998); G. M. T. Cheetham, D. Jeruzalmi, T. A. Steitz, Nature 399, 80 (1999).
    • (1998) Nature , vol.391 , pp. 304
    • Kiefer, J.R.1    Mao, C.2    Braman, J.C.3    Beese, L.S.4
  • 28
    • 0033529089 scopus 로고    scopus 로고
    • S. Doublie, S. Tabor, A. M. Long, C. C. Richardson, T. Ellenberger, Nature 391, 251 (1998); J. R. Kiefer, C. Mao, J. C. Braman, L. S. Beese, Nature 391, 304 (1998); G. M. T. Cheetham, D. Jeruzalmi, T. A. Steitz, Nature 399, 80 (1999).
    • (1999) Nature , vol.399 , pp. 80
    • Cheetham, G.M.T.1    Jeruzalmi, D.2    Steitz, T.A.3
  • 29
    • 0342537343 scopus 로고    scopus 로고
    • note
    • To generate the TEC model, a 15-bp double-stranded, B-DNA fragment (corresponding to the downstream duplex DNA from +3 to +17) and a 9-bp RNA/ DNA hybrid (16) were positioned manually into the Taq core RNAP crystal structure (6) [Protein Data Bank (PDB) ID 1DDQ] in a manner consistent with the cross-linking data (Fig. 2) by using the program O [T. A. Jones, J.-Y. Zou, S. Cowan, M. Kjeldgaard, Acta Crystallogr. A47, 110 (1991)]. Selected cross-links were specified as nuclear Overhauser enhancement-type distance constraints (with a 7 Å distance between the modified backbone phosphate and the appropriate protein atoms for the nonspecific cross-linking reagent, and a 3 Å length for the Lys-specific reagent), and a rigid-body energy minimization was performed to minimize steric clashes and maximize the correspondence with the distance constraints by using CNS [P. D. Adams, N. S. Pannu, R. J. Read, A. T. Brunger, Proc. Natl. Acad. Sci. U.S.A. 94, 5018 (1997)]. Only cross-links mapped to single amino acids or to protein fragments with relatively small exposed surfaces were used for the distance constraints. After this initial refinement, the additional segments of the nucleic acid framework were modeled manually. A second energy minimization was then performed in which the downstream duplex DNA and RNA/DNA hybrid were fixed in order to regularize the bond geometry and minimize steric clashes. Some additional distance constraints were introduced for the upstream single-strand RNA at this stage, in accordance with the cross-linking data.
  • 31
    • 0343406865 scopus 로고    scopus 로고
    • note
    • The label Ec preceding amino acid numbers indicates E. coli numbering, Ta indicates Taq numbering. If no indication is given, E. coli numbering is assumed.
  • 32
    • 0343842818 scopus 로고    scopus 로고
    • note
    • The evolutionarily conserved segments of the large β′ and β subunits (regions A to H and A to I, respectively) have been defined previously (1, 6).
  • 33
    • 0023749808 scopus 로고
    • D. J. Jin and C. A. Gross, J. Mol. Biol. 202, 45 (1988); K. Severinov, M. Soushko, A. Goldfarb, V. Nikiforov, Mol. Gen. Genet. 244, 120 (1994).
    • (1988) J. Mol. Biol. , vol.202 , pp. 45
    • Jin, D.J.1    Gross, C.A.2
  • 39
    • 0023905791 scopus 로고
    • S. Lynn, L. Kasper, J. Gardner, J. Biol. Chem. 263, 472 (1988); S.-W. Cheng et al., Science 254, 1205 (1992); K. Wilson and P. von Hippel, Proc. Natl. Acad. Sci. U.S.A. 92, 8793 (1995).
    • (1988) J. Biol. Chem. , vol.263 , pp. 472
    • Lynn, S.1    Kasper, L.2    Gardner, J.3
  • 40
    • 0026332799 scopus 로고
    • S. Lynn, L. Kasper, J. Gardner, J. Biol. Chem. 263, 472 (1988); S.-W. Cheng et al., Science 254, 1205 (1992); K. Wilson and P. von Hippel, Proc. Natl. Acad. Sci. U.S.A. 92, 8793 (1995).
    • (1992) Science , vol.254 , pp. 1205
    • Cheng, S.-W.1
  • 41
    • 0029073396 scopus 로고
    • S. Lynn, L. Kasper, J. Gardner, J. Biol. Chem. 263, 472 (1988); S.-W. Cheng et al., Science 254, 1205 (1992); K. Wilson and P. von Hippel, Proc. Natl. Acad. Sci. U.S.A. 92, 8793 (1995).
    • (1995) Proc. Natl. Acad. Sci. U.S.A. , vol.92 , pp. 8793
    • Wilson, K.1    Von Hippel, P.2
  • 42
    • 0033120034 scopus 로고    scopus 로고
    • I. Gusarov and E. Nudler, Mol. Cell 3, 495 (1999); W. S. Yarnell and J. W. Roberts, Science 284, 611 (1999).
    • (1999) Mol. Cell , vol.3 , pp. 495
    • Gusarov, I.1    Nudler, E.2
  • 43
    • 0033597435 scopus 로고    scopus 로고
    • I. Gusarov and E. Nudler, Mol. Cell 3, 495 (1999); W. S. Yarnell and J. W. Roberts, Science 284, 611 (1999).
    • (1999) Science , vol.284 , pp. 611
    • Yarnell, W.S.1    Roberts, J.W.2
  • 45
    • 0026317447 scopus 로고    scopus 로고
    • S. Borukhov, J. Lee, A. Goldfarb, J. Biol. Chem. 266, 23932 (1991); V. Markovtsov, A. Mustaev, A. Goldfarb, Proc. Natl. Acad. Sci. U.S.A. 93, 3221 (1996); V. Epshtein et al., in preparation.
    • (1991) J. Biol. Chem. , vol.266 , pp. 23932
    • Borukhov, S.1    Lee, J.2    Goldfarb, A.3
  • 47
    • 0026317447 scopus 로고    scopus 로고
    • in preparation
    • S. Borukhov, J. Lee, A. Goldfarb, J. Biol. Chem. 266, 23932 (1991); V. Markovtsov, A. Mustaev, A. Goldfarb, Proc. Natl. Acad. Sci. U.S.A. 93, 3221 (1996); V. Epshtein et al., in preparation.
    • Epshtein, V.1
  • 51
    • 9344221087 scopus 로고    scopus 로고
    • E. Zaychikov et al., Science 273, 107 (1996); A. Mustaev et al., Proc. Natl. Acad. Sci. U.S.A. 94, 6641 (1997).
    • (1996) Science , vol.273 , pp. 107
    • Zaychikov, E.1
  • 53
    • 0026346986 scopus 로고
    • S. Borukhov et al., J. Biol. Chem. 266, 23921 (1991); K. Severinov et al., J. Biol. Chem. 269, 14254 (1994).
    • (1991) J. Biol. Chem. , vol.266 , pp. 23921
    • Borukhov, S.1
  • 54
    • 0028270742 scopus 로고
    • S. Borukhov et al., J. Biol. Chem. 266, 23921 (1991); K. Severinov et al., J. Biol. Chem. 269, 14254 (1994).
    • (1994) J. Biol. Chem. , vol.269 , pp. 14254
    • Severinov, K.1
  • 58
    • 0029861154 scopus 로고    scopus 로고
    • K. Severinov et al., Proc. Natl. Acad. Sci. U.S.A. 92, 4591 (1995); K. Severinov et al., J. Biol. Chem. 271, 27969 (1996).
    • (1996) J. Biol. Chem. , vol.271 , pp. 27969
    • Severinov, K.1
  • 59
    • 0026319199 scopus 로고    scopus 로고
    • note
    • Figures 3 and 4 were made with the program GRASP [A. Nicholls, K. A. Sharp, B. Honig, Prot. Struct. Funct. Genet. 11, 281 (1991)]. We thank K. Severinov for the strain overproducing the Xho 19 β subunit mutant and M. Chlenov for participation in development of the DNA-protein cross-linking methods. Supported in part by NIH grants GM30717 and GM49242 (to A.G.) and NIH grant GM53759 (to S.A.D.).


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