Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS

Molecular Cell

Volumn 16, Issue 6, 2004, Pages 955-965

  Kettenberger, Hubert ^a   Armache, Karim Jean ^a   Cramer, Patrick ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA HYBRID; ELONGATION FACTOR; NUCLEOSIDE TRIPHOSPHATE; RNA POLYMERASE; RNA POLYMERASE II;

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; DNA TEMPLATE; NONHUMAN; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DNA; MOLECULAR SEQUENCE DATA; NUCLEOTIDES; PROTEIN STRUCTURE, TERTIARY; RNA; RNA POLYMERASE II; TRANSCRIPTIONAL ELONGATION FACTORS; YEASTS;

EID: 10944232674     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2004.11.040     Document Type: Article

References (47)

1. Armache K.-J., Kettenberger H., Cramer P. Architecture of the initiation-competent 12-subunit RNA polymerase II. Proc. Natl. Acad. Sci. USA. 100:2003;6964-6968
2. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., et al. Crystallography &NMR system. A new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921
3. Bushnell D.A., Kornberg R.D. Complete RNA polymerase II at 4.1 Å resolution. implications for the initiation of transcription Proc. Natl. Acad. Sci. USA. 100:2003;6969-6972
4. Bushnell D.A., Westover K.D., Davis R.E., Kornberg R.D. Structural basis of transcription. an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms Science. 303:2004;983-988
5. Chen H.T., Hahn S. Binding of TFIIB to RNA polymerase II. mapping the binding site for the TFIIB zinc ribbon domain within the preinitiation complex Mol. Cell. 12:2003;437-447
6. Chen H.T., Hahn S. Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex. a model for the structure of the PIC Cell. 119:2004;169-180
7. Chung W.H., Craighead J.L., Chang W.H., Ezeokonkwo C., Bareket-Samish A., Kornberg R.D., Asturias F.J. RNA polymerase II/TFIIF structure and conserved organization of the initiation complex. Mol. Cell. 12:2003;1003-1013
8. Craighead J.L., Chang W.H., Asturias F.J. Structure of yeast RNA polymerase II in solution. implications for enzyme regulation and interaction with promoter DNA Struct. Fold. Des. 10:2002;1117-1125
9. Cramer P. RNA polymerase II structure. from core to functional complexes Curr. Opin. Genet. Dev. 14:2004;218-226. a
10. Cramer P. Structure and function of RNA polymerase II. Adv. Protein Chem. 67:2004;1-42. b
11. Cramer P., Bushnell D.A., Fu J., Gnatt A.L., Maier-Davis B., Thompson N.E., Burgess R.R., Edwards A.M., David P.R., Kornberg R.D. Architecture of RNA polymerase II and implications for the transcription mechanism. Science. 288:2000;640-649
12. Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription. RNA polymerase II at 2.8 angstrom resolution Science. 292:2001;1863-1876
13. Erie D.A. The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription. Biochim. Biophys. Acta. 1577:2002;224-239
14. Fish R.N., Kane C.M. Promoting elongation with transcript cleavage stimulatory factors. Biochim. Biophys. Acta. 1577:2002;287-307
15. Forget D., Langelier M.F., Therien C., Trinh V., Coulombe B. Photo-cross-linking of a purified preinitiation complex reveals central roles for the RNA polymerase II mobile clamp and TFIIE in initiation mechanisms. Mol. Cell. Biol. 24:2004;1122-1131
16. Gnatt A. Elongation by RNA polymerase II. structure-function relationship Biochim. Biophys. Acta. 1577:2002;175-190
17. Gnatt A., Fu J., Kornberg R.D. Formation and crystallization of yeast RNA polymerase II elongation complexes. J. Biol. Chem. 272:1997;30799-30805
18. 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 A resolution Science. 292:2001;1876-1882
19. Kettenberger H., Armache K.-J., Cramer P. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell. 114:2003;347-357
20. Kim T.K., Ebright R.H., Reinberg D. Mechanism of ATP-dependent promoter melting by transcription factor IIH. Science. 288:2000;1418-1422
21. Kireeva M.L., Komissarova N., Kashlev M. Overextended RNA:DNA hybrid as a negative regulator of RNA polymerase II processivity. J. Mol. Biol. 299:2000;325-335. a
22. Kireeva M.L., Komissarova N., Waugh D.S., Kashlev M. The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J. Biol. Chem. 275:2000;6530-6536. b
23. Korzheva N., Mustaev A., Kozlov M., Malhotra A., Nikiforov V., Goldfarb A., Darst S.A. A structural model of transcription elongation. Science. 289:2000;619-625
24. Landick R. Active-site dynamics in RNA polymerases. Cell. 116:2004;351-353
25. Meinhart A., Blobel J., Cramer P. An extended winged helix domain in general transcription factor E/IIEα J. Biol. Chem. 278:2003;48267-48274
26. Murakami K.S., Masuda S., Campbell E.A., Muzzin O., Darst S.A. Structural basis of transcription initiation. an RNA polymerase holoenzyme-DNA complex Science. 296:2002;1285-1290
27. Naryshkin N., Revyakin A., Kim Y., Mekler V., Ebright R.H. Structural organization of the RNA polymerase-promoter open complex. Cell. 101:2000;601-611
28. Nudler E. Transcription elongation. structural basis and mechanisms J. Mol. Biol. 288:1999;1-12
29. Nudler E., Avetissova E., Markovtsov V., Goldfarb A. Transcription processivity. Protein-DNA interactions holding together the elongation complex Science. 273:1996;211-217
30. Nudler E., Gusarov I., Avetissova E., Kozlov M., Goldfarb A. Spatial organization of transcription elongation complex in Escherichia coli. Science. 281:1998;424-428
31. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Meth Enzym. 276:1996;307-326
32. Palangat M., Meier T.I., Keene R.G., Landick R. Transcriptional pausing at +62 of HIV-1 nascent RNA modulates formation of the TAR RNA structure. Mol. Cell. 1:1998;1033-1042
33. Palangat M., Hittinger C.T., Landick R. Downstream DNA selectively affects a paused conformation of human RNA polymerase II. J. Mol. Biol. 341:2004;429-442
34. Poglitsch C.L., Meredith G.D., Gnatt A.L., Jensen G.J., Chang W.H., Fu J., Kornberg R.D. Electron crystal structure of an RNA polymerase II transcription elongation complex. Cell. 98:1999;791-798
35. Shilatifard A., Conaway R.C., Conaway J.W. The RNA polymerase II elongation complex. Annu. Rev. Biochem. 72:2003;693-715
36. Sosunov V., Sosunova E., Mustaev A., Bass I., Nikiforov V., Goldfarb A. Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. EMBO J. 22:2003;2234-2244
37. Steitz T.A. The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase. Curr. Opin. Struct. Biol. 14:2004;4-9
38. Svetlov V., Vassylyev D.G., Artsimovitch I. Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase. J. Biol. Chem. 279:2004;38087-38090
39. Tahirov T.H., Temiakov D., Anikin M., Patlan V., McAllister W.T., Vassylyev D.G., Yokoyama S. Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution. Nature. 420:2002;43-50
40. Temiakov D., Patlan V., Anikin M., McAllister W.T., Yokoyama S., Vassylyev D.G. Structural basis for substrate selection by t7 RNA polymerase. Cell. 116:2004;381-391
41. Werner F., Weinzierl R.O. A recombinant RNA polymerase II-like enzyme capable of promoter-specific transcription. Mol. Cell. 10:2002;635-646
42. Westover K.D., Bushnell D.A., Kornberg R.D. Structural basis of transcription. separation of RNA from DNA by RNA polymerase II Science. 303:2004;1014-1016. a
43. Westover K.D., Bushnell D.A., Kornberg R.D. Structural basis of transcription. nucleotide selection by rotation in the RNA polymerase II active center Cell. 119:2004;481-489. b
44. Wind M., Reines D. Transcription elongation factor SII. Bioessays. 22:2000;327-336
45. Yin Y.W., Steitz T.A. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science. 298:2002;1387-1395
46. Yin Y.W., Steitz T.A. The structural mechanism of translocation and helicase activity in t7 RNA polymerase. Cell. 116:2004;393-404
47. Zhang C., Burton Z.F. Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism. J. Mol. Biol. 342:2004;1085-1099