Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein

Nature

Volumn 468, Issue 7326, 2010, Pages 978-982

  Tagami, Shunsuke ^a,b   Sekine, Shun Ichi ^a,b   Kumarevel, Thirumananseri ^c   Hino, Nobumasa ^b   Murayama, Yuko ^a,b   Kamegamori, Syunsuke ^a,b   Yamamoto, Masaki ^c   Sakamoto, Kensaku ^b   Yokoyama, Shigeyuki ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b RIKEN   (Japan)

^c Harima Institute ^*  (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ELONGATION FACTOR; NUCLEOSIDE TRIPHOSPHATE; PHOSPHATE; RNA POLYMERASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GFH1; UNCLASSIFIED DRUG;

CRYSTAL; ENZYME ACTIVITY; GENE EXPRESSION; PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CATALYSIS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; GENE TRANSLOCATION; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; THERMUS THERMOPHILUS; TRANSCRIPTION TERMINATION;

BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DNA; DNA-DIRECTED RNA POLYMERASES; MODELS, MOLECULAR; PROTEIN CONFORMATION; THERMUS THERMOPHILUS; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); THERMUS; THERMUS THERMOPHILUS;

EID: 78650310283     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature09573     Document Type: Article

References (41)

1. Borukhov, S., Polyakov, A., Nikiforov, V. & Goldfarb, A. GreA protein: a transcription elongation factor from Escherichia coli. Proc. Natl Acad. Sci. USA 89, 8899-8902 (1992).
2. Stebbins, C. E. et al. Crystal structure of the GreA transcript cleavage factor from Escherichia coli. Nature 373, 636-640 (1995).
3. Vassylyeva, M. N. et al. The carboxy-terminal coiled-coil of the RNA polymerase b'-subunit is the main binding site for Gre factors. EMBO Rep. 8, 1038-1043 (2007).
4. Hogan, B. P., Hartsch, T. & Erie, D. A. Transcript cleavage by Thermus thermophilus RNA polymerase. Effects of GreA and anti-GreA factors. J. Biol. Chem. 277, 967-975 (2002).
5. Laptenko, O. & Borukhov, S. Biochemical assays of Gre factors of Thermus thermophilus. Methods Enzymol. 371, 219-232 (2003).
6. Lamour, V., Hogan, B. P., Erie, D. A. & Darst, S. A. Crystal structure of Thermus aquaticus Gfh1, A Gre-factor paralog that inhibits rather than stimulates transcript cleavage. J. Mol. Biol. 356, 179-188 (2006).
7. Laptenko, O. et al. PH-dependent conformational switch activates the inhibitor of transcription elongation. EMBO J. 25, 2131-2141 (2006).
8. Symersky, J. et al. Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors. J. Biol. Chem. 281, 1309-1312 (2006).
9. Zhang, G. et al. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A? resolution. Cell 98, 811-824 (1999).
10. Cramer, P., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292, 1863-1876 (2001).
11. Vassylyev, D. G. et al. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A? resolution. Nature 417, 712-719 (2002).
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, 1876-1882 (2001). (Pubitemid 32538357)
13. Vassylyev, D. G., Vassylyeva, M. N., Perederina, A., Tahirov, T. H. & Artsimovitch, I. Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448, 157-162 (2007). (Pubitemid 47067370)
14. Vassylyev, D. G. et al. Structural basis for substrate loading in bacterial RNA polymerase. Nature 448, 163-168 (2007).
15. 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. Cell 127, 941-954 (2006).
16. Westover, K. D., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science 303, 1014-1016 (2004).
17. 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, 481-489 (2004).
18. Kettenberger, H., Armache, K. J. & Cramer, P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 16, 955-965 (2004).
19. Brueckner, F. & Cramer, P. Structural basis of transcription inhibition by a-amanitin and implications for RNA polymerase II translocation. Nature Struct. Mol. Biol. 15, 811-818 (2008).
20. Sydow, J. F. et al. Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol. Cell 34, 710-721 (2009).
21. Wang, D. et al. Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science 324, 1203-1206 (2009).
22. Temiakov, D. et al. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol. Cell 19, 655-666 (2005).
23. Tuske, S. et al. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell 122, 541-552 (2005).
24. Tagami, S., Sekine, S., Kumarevel, T., Yamamoto, M. & Yokoyama, S. Crystallization and preliminary X-ray crystallographic analysis of Thermus thermophilus transcription elongation complex bound to Gfh1. Acta Crystallogr. F 66, 64-68 (2010).
25. Darst, S. A. et al. Conformational flexibility of bacterial RNA polymerase. Proc. Natl Acad. Sci. USA 99, 4296-4301 (2002).
26. Murakami, K. S.,Masuda, S.&Darst, S. A. Structural basis of transcriptioninitiation: RNA polymerase holoenzyme at 4 A? resolution. Science 296, 1280-1284 (2002). (Pubitemid 34522777)
27. Tan, L., Wiesler, S., Trzaska, D., Carney, H. C. & Weinzierl, R. O. Bridge helix and trigger loop perturbations generate superactive RNA polymerases. J. Biol. 7, 40 (2008).
28. Kettenberger, H., Armache, K. J. & Cramer, P. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell 114, 347-357 (2003).
29. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004).
30. Brunger, A. T.Version1.2 of the Crystallography andNMRsystem.Nature Protocols 2, 2728-2733 (2007).
31. Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795-800 (1993).
32. McCoy, A. J. et al.Phaser crystallographic software. J.Appl. Crystallogr.40, 658-674 (2007).
33. Brünger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
34. Mukhopadhyay, J. et al. The RNA polymerase "switch region" is a target for inhibitors. Cell 135, 295-307 (2008).
35. Abyzov, A., Bjornson, R., Felipe, M. & Gerstein, M. RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes. Proteins 78, 309-324 (2010).
36. Vassylyeva, M. N. et al. Purification, Crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus. Acta Crystallogr. D 58, 1497-1500 (2002).
37. Kashkina, E. et al. Elongation complexes of Thermus thermophilusRNA polymerase that possess distinct translocation conformations. Nucleic Acids Res. 34, 4036-4045 (2006).
38. Chin, J. W., Martin, A. B., King, D. S., Wang, L. & Schultz, P. G. Addition of a photocrosslinking amino acid to the genetic code of Escherichia coli. Proc. Natl Acad. Sci. USA 99, 11020-11024 (2002). (Pubitemid 34920872)
39. Sakamoto, K. et al. Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography. Structure 17, 335-344 (2009).
40. Chumpolkulwong, N. et al. Translation of 'rare' codons in a cell-free protein synthesis system from Escherichia coli. J. Struct. Funct. Genomics 7, 31-36 (2006).
41. Hino, N. et al. Protein photo-cross-linking in mammalian cells by sitespecific incorporation of a photoreactive amino acid. Nature Methods 2, 201-206 (2005).