Structural basis of transcription: Nucleotide selection by rotation in the RNA polymerase II active center

Cell

Volumn 119, Issue 4, 2004, Pages 481-489

  Westover, Kenneth D ^a   Bushnell, David A ^a   Kornberg, Roger D ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOENZYME; NUCLEOTIDE; RIBONUCLEOSIDE DERIVATIVE; RIBONUCLEOSIDE TRIPHOSPHATE; RNA POLYMERASE II; UNCLASSIFIED DRUG;

ARTICLE; BASE MISPAIRING; BINDING SITE; CRYSTAL; DNA HELIX; DNA TEMPLATE; ENZYME ACTIVE SITE; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; ROTATION; X RAY CRYSTALLOGRAPHY;

EID: 8344234112     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2004.10.016     Document Type: Article

References (32)

1. Artsimovitch I., Patlan V., Sekine S., Vassylyeva M.N., Hosaka T., Ochi K., Yokoyama S., Vassylyev D.G. Structural basis for transcription regulation by alarmone ppGpp. Cell. 117:2004;299-310
2. Bonner G., Lafer E.M., Sousa R. Characterization of a set of T7 RNA polymerase active site mutants. J. Biol. Chem. 269:1994;25120-25128
3. Brieba L.G., Sousa R. Roles of histidine 784 and tyrosine 639 in ribose discrimination by T7 RNA polymerase. Biochemistry. 39:2000;919-923
4. 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
5. 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
6. 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
7. Doublie S., Tabor S., Long A.M., Richardson C.C., Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature. 391:1998;251-258
8. Dudev T., Lim C. Principles governing Mg, Ca, and Zn binding and selectivity in proteins. Chem. Rev. 103:2003;773-788
9. Epshtein V., Mustaev A., Markovtsov V., Bereshchenko O., Nikiforov V., Goldfarb A. Swing-gate model of nucleotide entry into the RNA polymerase active center. Mol. Cell. 10:2002;623-634
10. Fish R.N., Kane C.M. Promoting elongation with transcript cleavage stimulatory factors. Biochim. Biophys. Acta. 1577:2002;287-307
11. Foster J.E., Holmes S.F., Erie D.A. Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation. Cell. 106:2001;243-252
12. 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
13. Gu W., Reines D. Variation in the size of nascent RNA cleavage products as a function of transcript length and elongation competence. J. Biol. Chem. 270:1995;30441-30447
14. Huang Y., Eckstein F., Padilla R., Sousa R. Mechanism of ribose 2′-group discrimination by an RNA polymerase. Biochemistry. 36:1997;8231-8242
15. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47(Pt 2):1991;110-119
16. 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
17. 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
18. Leslie, A. (1992). Joint CCP4 and ESF-EACMB Newsletter, No. 26 (Warrington, United Kindgom: Daresbury Laboratory).
19. Murshudov G.N., Lebedev A., Vagin A.A., Wilson K.S., Dodson E.J. Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr. D. 55:1999;247-255
20. Opalka N., Chlenov M., Chacon P., Rice W.J., Wriggers W., Darst S.A. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell. 114:2003;335-345
21. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1996;307-326
22. Patel P.H., Suzuki M., Adman E., Shinkai A., Loeb L.A. Prokaryotic DNA polymerase I. evolution, structure, and "base flipping" mechanism for nucleotide selection J. Mol. Biol. 308:2001;823-837
23. Santangelo T.J., Roberts J.W. Forward translocation is the natural pathway of RNA release at an intrinsic terminator. Mol. Cell. 14:2004;117-126
24. Shi Y.B., Gamper H., Van Houten B., Hearst J.E. Interaction of Escherichia coli RNA polymerase with DNA in an elongation complex arrested at a specific psoralen crosslink site. J. Mol. Biol. 199:1988;277-293
25. 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
26. Steitz T.A. A mechanism for all polymerases. Nature. 391:1998;231-232
27. 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
28. Temiakov D., Tahirov T.H., Anikin M., McAllister W.T., Vassylyev D.G., Yokoyama S. Crystallization and preliminary crystallographic analysis of T7 RNA polymerase elongation complex. Acta Crystallogr. D Biol. Crystallogr. 59:2003;185-187
29. 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
30. 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
31. Yin Y.W., Steitz T.A. The structural mechanism of translocation and helicase activity in t7 RNA polymerase. Cell. 116:2004;393-404
32. Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell. 98:1999;811-824