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1
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0037071844
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Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution
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Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., and Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 417 (2002) 712-719
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Nature
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Vassylyev, D.G.1
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1142274214
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Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms
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Bushnell D.A., Westover K.D., Davis R.E., and Kornberg R.D. Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms. Science 303 (2004) 983-988
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Bushnell, D.A.1
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34447499995
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Structural basis for transcription elongation by bacterial RNA polymerase
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This paper reports the 2.5 Å resolution structure of the T. thermophilus elongation complex that provided a number of crucial mechanistic insights in the basic principles of transcription and revealed the key determinants in RNAP essential for fidelity, stability and processivity of transcription elongation.
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Vassylyev D.G., Vassylyeva M.N., Perederina A., Tahirov T.H., and Artsimovitch I. Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448 (2007) 157-162. This paper reports the 2.5 Å resolution structure of the T. thermophilus elongation complex that provided a number of crucial mechanistic insights in the basic principles of transcription and revealed the key determinants in RNAP essential for fidelity, stability and processivity of transcription elongation.
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Nature
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Vassylyev, D.G.1
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Tahirov, T.H.4
Artsimovitch, I.5
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4
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34447513771
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Structural basis for substrate loading in bacterial RNA polymerase
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The 3.0A resolution structures of the two bacterial ECs with the substrate analog revealed the inactive (pre-insertion) and active (insertion) substrate intermediates and provided an evidence for the two-step mechanism of substrate loading in the bacterial enzyme. The structures showed that isomerization from the inactive, open (pre-insertion) complex to the catalytically active closed (insertion) state occurs via substrate-induced folding of the TL. The antibiotic streptolydigin prevents proper folding of the TL thereby freezing the substrate complex in the inactive, pre-insertion configuration.
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Vassylyev D.G., Vassylyeva M.N., Zhang J., Palangat M., Artsimovitch I., and Landick R. Structural basis for substrate loading in bacterial RNA polymerase. Nature 448 (2007) 163-168. The 3.0A resolution structures of the two bacterial ECs with the substrate analog revealed the inactive (pre-insertion) and active (insertion) substrate intermediates and provided an evidence for the two-step mechanism of substrate loading in the bacterial enzyme. The structures showed that isomerization from the inactive, open (pre-insertion) complex to the catalytically active closed (insertion) state occurs via substrate-induced folding of the TL. The antibiotic streptolydigin prevents proper folding of the TL thereby freezing the substrate complex in the inactive, pre-insertion configuration.
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Nature
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Vassylyev, D.G.1
Vassylyeva, M.N.2
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Artsimovitch, I.5
Landick, R.6
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5
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0035827332
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Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution
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Gnatt A.L., Cramer P., Fu J., Bushnell D.A., and Kornberg R.D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 292 (2001) 1876-1882
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Gnatt, A.L.1
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10944232674
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Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
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The authors present a medium resolution structure of the EC formed by yeast RNA polymerase II. The structure of the EC with bound NTP analog provided the first experimental evidence for the pre-insertion substrate intermediate in the eukaryotic system.
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Kettenberger H., Armache K.J., and Cramer P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell 16 (2004) 955-965. The authors present a medium resolution structure of the EC formed by yeast RNA polymerase II. The structure of the EC with bound NTP analog provided the first experimental evidence for the pre-insertion substrate intermediate in the eukaryotic system.
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Mol Cell
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Kettenberger, H.1
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Structural basis of transcription: separation of RNA from DNA by RNA polymerase II
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Westover K.D., Bushnell D.A., and Kornberg R.D. Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science 303 (2004) 1014-1016
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8344234112
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Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center
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Westover K.D., Bushnell D.A., and Kornberg R.D. Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell 119 (2004) 481-489
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Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis
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In this work, the authors reported a number of the eukaryotic ECs with different (cognate and non-cognate NTPs) and demonstrated that structural reconfiguration of the TL mediates closure of the active site in the presence of the cognate NTP in the yeast enzyme in a similar fashion of that of the bacterial system.
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Wang D., Bushnell D.A., Westover K.D., Kaplan C.D., and Kornberg R.D. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127 (2006) 941-954. In this work, the authors reported a number of the eukaryotic ECs with different (cognate and non-cognate NTPs) and demonstrated that structural reconfiguration of the TL mediates closure of the active site in the presence of the cognate NTP in the yeast enzyme in a similar fashion of that of the bacterial system.
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Wang, D.1
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Brueckner, F.1
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Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution
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Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA
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Sydow J.F., Brueckner F., Cheung A.C.M., Damsma G.E., Dengl S., Lehmann E., Vassylyev D.G., and Cramer P. Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol. Cell. 34 (2009) 710-721
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The structure of the yeast EC with bound toxin, α-amanitin revealed the important, pre-templated translocation intermediate and suggested the essential roles of the bridge helix and TL in translocation.
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Brueckner F., and Cramer P. Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat Struct Mol Biol 15 (2008) 811-818. The structure of the yeast EC with bound toxin, α-amanitin revealed the important, pre-templated translocation intermediate and suggested the essential roles of the bridge helix and TL in translocation.
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The structure of eukaryotic RNAP complexed with α-amanitin and subsequent biochemical data demonstrated that the TL is an important determinant of transcription fidelity.
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Kaplan, C.D.1
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Artsimovitch I., Patlan V., Sekine S., Vassylyeva M.N., Hosaka T., Ochi K., Yokoyama S., and Vassylyev D.G. Structural basis for transcription regulation by alarmone ppGpp. Cell 117 (2004) 299-310
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Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins
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Artsimovitch I., Vassylyeva M.N., Svetlov D., Svetlov V., Perederina A., Igarashi N., Matsugaki N., Wakatsuki S., Tahirov T.H., and Vassylyev D.G. Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell 122 (2005) 351-363
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24044497229
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Structural basis of transcription inhibition by antibiotic streptolydigin
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Temiakov D., Zenkin N., Vassylyeva M.N., Perederina A., Tahirov T.H., Kashkina E., Savkina M., Zorov S., Nikiforov V., Igarashi N., et al. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell 19 (2005) 655-666
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Igarashi, N.10
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28544453415
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Structural basis for transcription inhibition by tagetitoxin
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Vassylyev D.G., Svetlov V., Vassylyeva M.N., Perederina A., Igarashi N., Matsugaki N., Wakatsuki S., and Artsimovitch I. Structural basis for transcription inhibition by tagetitoxin. Nat Struct Mol Biol 12 (2005) 1086-1093
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Nat Struct Mol Biol
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The structure of the bacterial RNAP holoenzyme in complex with antibiotic myxopyronin revealed that refolding of the switch-2 segment mediates downstream propagation of the transcription bubble during open complex formation. The data suggest that the conformational transitions of the switch-2 may play an essential regulatory role.
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Belogurov G.A., Vassylyeva M.N., Sevostyanova A., Appleman J.R., Xiang A.X., Lira R., Webber S.E., Klyuyev S., Nudler E., Artsimovitch I., et al. Transcription inactivation through local refolding of the RNA polymerase structure. Nature 457 (2009) 332-335. The structure of the bacterial RNAP holoenzyme in complex with antibiotic myxopyronin revealed that refolding of the switch-2 segment mediates downstream propagation of the transcription bubble during open complex formation. The data suggest that the conformational transitions of the switch-2 may play an essential regulatory role.
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Nature
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Belogurov, G.A.1
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The structure of RfaH allowed to elucidate mechanism of action of this transcription factor in which the protein undergoes DNA-dependent activation via the domain dissociation that is required to open the binding cavity and to form a stable complex with RNAP. The structural analysis also allowed to identify the β′-subunit clamp helices as the RfaH major binding site on RNAP to which the protein is recruited through the hydrophobic interactions.
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