Structural basis of transcription inhibition by α-amanitin and implications for RNA polymerase II translocation (original) (raw)
References
Gnatt, A.L., Cramer, P., Fu, J., Bushnell, D.A. & Kornberg, R.D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution. Science292, 1876–1882 (2001). ArticleCASPubMed Google Scholar
Kettenberger, H., Armache, K.-J. & Cramer, P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell16, 955–965 (2004). ArticleCASPubMed Google Scholar
Westover, K.D., Bushnell, D.A. & Kornberg, R.D. Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell119, 481–489 (2004). ArticleCASPubMed Google Scholar
Wang, D., Bushnell, D.A., Westover, K.D., Kaplan, C.D. & Kornberg, R.D. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell127, 941–954 (2006). ArticleCASPubMedPubMed Central Google Scholar
Cramer, P., Bushnell, D.A. & Kornberg, R.D. Structural basis of transcription: RNA polymerase II at 2.8 Å resolution. Science292, 1863–1876 (2001). ArticleCASPubMed Google Scholar
Vassylyev, D.G. et al. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature417, 712–719 (2002). ArticleCASPubMed Google Scholar
Bar-Nahum, G. et al. A ratchet mechanism of transcription elongation and its control. Cell120, 183–193 (2005). ArticleCASPubMed Google Scholar
Epshtein, V. et al. Swing-gate model of nucleotide entry into the RNA polymerase active center. Mol. Cell10, 623–634 (2002). ArticleCASPubMed Google Scholar
Tuske, S. et al. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell122, 541–552 (2005). ArticleCASPubMedPubMed Central Google Scholar
Artsimovitch, I. et al. Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell122, 351–363 (2005). ArticleCASPubMed Google Scholar
Bushnell, D.A., Cramer, P. & Kornberg, R.D. Structural basis of transcription: α-amanitin-RNA polymerase II cocrystal at 2.8 Å resolution. Proc. Natl. Acad. Sci. USA99, 1218–1222 (2002). ArticleCASPubMedPubMed Central Google Scholar
Gong, X.Q., Nedialkov, Y.A. & Burton, Z.F. α-amanitin blocks translocation by human RNA polymerase II. J. Biol. Chem.279, 27422–27427 (2004). ArticleCASPubMed Google Scholar
Vassylyev, D.G. et al. Structural basis for substrate loading in bacterial RNA polymerase. Nature448, 163–168 (2007). ArticleCASPubMed Google Scholar
Kashkina, E. et al. Multisubunit RNA polymerases melt only a single DNA base pair downstream of the active site. J. Biol. Chem.282, 21578–21582 (2007). ArticleCASPubMed Google Scholar
Vassylyev, D.G., Vassylyeva, M.N., Perederina, A., Tahirov, T.H. & Artsimovitch, I. Structural basis for transcription elongation by bacterial RNA polymerase. Nature448, 157–162 (2007). ArticleCASPubMed Google Scholar
Naji, S., Bertero, M.G., Spitalny, P., Cramer, P. & Thomm, M. Structure function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement. Nucleic Acids Res.36, 676–687 (2007). ArticlePubMedPubMed Central Google Scholar
Campbell, E.A. et al. Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase. EMBO J.24, 674–682 (2005). ArticleCASPubMedPubMed Central Google Scholar
Toulokhonov, I., Zhang, J., Palangat, M. & Landick, R. A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol. Cell27, 406–419 (2007). ArticleCASPubMed Google Scholar
Damsma, G.E., Alt, A., Brueckner, F., Carell, T. & Cramer, P. Mechanism of transcriptional stalling at cisplatin-damaged DNA. Nat. Struct. Mol. Biol.14, 1127–1133 (2007). ArticleCASPubMed Google Scholar
Temiakov, D. et al. Structural basis for substrate selection by T7 RNA polymerase. Cell116, 381–391 (2004). ArticleCASPubMed Google Scholar
Yin, Y.W. & Steitz, T.A. The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell116, 393–404 (2004). ArticleCASPubMed Google Scholar
Cramer, P. Common structural features of nucleic acid polymerases. Bioessays24, 724–729 (2002). ArticleCASPubMed Google Scholar
Abbondanzieri, E.A., Greenleaf, W.J., Shaevitz, J.W., Landick, R. & Block, S.M. Direct observation of base-pair stepping by RNA polymerase. Nature438, 460–465 (2005). ArticleCASPubMedPubMed Central Google Scholar
Galburt, E.A. et al. Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. Nature446, 820–823 (2007). ArticleCASPubMed Google Scholar
Chafin, D.R., Guo, H. & Price, D.H. Actions of α-amanitin during pyrophosphoryolysis and elongation by RNA polymerase II. J. Biol. Chem.270, 19114–19119 (1995). ArticleCASPubMed Google Scholar
Rudd, M.D. & Luse, D.S. Amanitin greatly reduces the rate of transcription by RNA polymerase II ternary complexes but fails to inhibit some transcript cleavage modes. J. Biol. Chem.271, 21549–21558 (1996). ArticleCASPubMed Google Scholar
Wienland, T. & Faulstich, H. Fifty years of amanitin. Experientia47, 1186–1193 (1991). Article Google Scholar
Zanotti, G., Petersen, G. & Wieland, T. Structure-toxicity relationships in the amatoxin series. Int. J. Pept. Protein Res.40, 551–558 (1992). ArticleCASPubMed Google Scholar
Armache, K.-J., Kettenberger, H. & Cramer, P. Architecture of the initiation-competent 12-subunit RNA polymerase II. Proc. Natl. Acad. Sci. USA100, 6964–6968 (2003). ArticleCASPubMedPubMed Central Google Scholar
Brueckner, F., Hennecke, U., Carell, T. & Cramer, P. CPD damage recognition by transcribing RNA polymerase II. Science315, 859–862 (2007). ArticleCASPubMed Google Scholar
Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr.26, 795–800 (1993). ArticleCAS Google Scholar
McCoy, A.J., Grosse-Kunstleve, R.W., Storoni, L.C. & Read, R.J. Likelihood-enhanced fast translation functions. Acta Crystallogr. D Biol. Crystallogr.61, 458–464 (2005). ArticlePubMed Google Scholar
Brunger, A.T. Version 1.2 of the Crystallography and NMR system. Nat. Protocols2, 2728–2733 (2007). ArticleCASPubMed Google Scholar
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr.60, 2126–2132 (2004). ArticlePubMed Google Scholar
Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47, 110–119 (1991). ArticlePubMed Google Scholar
Gerber, P.R. & Muller, K. MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry. J. Comput. Aided Mol. Des.9, 251–268 (1995). ArticleCASPubMed Google Scholar
Armache, K.-J., Mitterweger, S., Meinhart, A. & Cramer, P. Structures of complete RNA polymerase II and its subcomplex Rpb4/7. J. Biol. Chem.280, 7131–7134 (2005). ArticleCASPubMed Google Scholar
Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr.26, 283–291 (1993). ArticleCAS Google Scholar