Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution
10.1126/science.1069594
Crossref journal-article
American Association for the Advancement of Science (AAAS)
Science (221)
Abstract

The crystal structure of the initiating form of Thermus aquaticus RNA polymerase, containing core RNA polymerase (α 2 ββ′ω) and the promoter specificity σ subunit, has been determined at 4 angstrom resolution. Important structural features of the RNA polymerase and their roles in positioning σ within the initiation complex are delineated, as well as the role played by σ in modulating the opening of the RNA polymerase active-site channel. The two carboxyl-terminal domains of σ are separated by 45 angstroms on the surface of the RNA polymerase, but are linked by an extended loop. The loop winds near the RNA polymerase active site, where it may play a role in initiating nucleotide substrate binding, and out through the RNA exit channel. The advancing RNA transcript must displace the loop, leading to abortive initiation and ultimately to σ release.

Bibliography

Murakami, K. S., Masuda, S., & Darst, S. A. (2002). Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution. Science, 296(5571), 1280–1284.

Authors 3
  1. Katsuhiko S. Murakami (first)
  2. Shoko Masuda (additional)
  3. Seth A. Darst (additional)
References 45 Referenced 485
  1. 10.1126/science.1059493
  2. Darst S. A., Curr. Opin. Struct. Biol. 11, 155 (2001). (10.1016/S0959-440X(00)00185-8) / Curr. Opin. Struct. Biol. by Darst S. A. (2001)
  3. G. Zhang et al. Cell 98 811 (1999). (10.1016/S0092-8674(00)81515-9)
  4. 10.1016/S0962-8924(99)01679-7
  5. Reviewed in C. A. Gross et al. Cold Spring Harbor Symp. Quant. Biol. 63 141 (1998).
  6. 10.1128/JB.180.12.3019-3025.1998
  7. 10.1021/bi00555a023
  8. McClure W. R., Cech C. L., Johnston D. E., J. Biol. Chem. 253, 8941 (1978). (10.1016/S0021-9258(17)34268-0) / J. Biol. Chem. by McClure W. R. (1978)
  9. Mustaev A., Korzheva N., Curr. Opin. Microbiol. 4, 119 (2001). (10.1016/S1369-5274(00)00176-4) / Curr. Opin. Microbiol. by Mustaev A. (2001)
  10. E. A. Campbell et al. Cell 104 901 (2001). (10.1016/S0092-8674(01)00286-0)
  11. E. A. Campbell et al. Mol. Cell 9 527 (2002). (10.1016/S1097-2765(02)00470-7)
  12. Supplementary material is available on Science Online at www.sciencemag.org/cgi/content/full/296/5571/1280/DC1.
  13. Gruber T. M., Bryant D. A., J. Bacteriol. 179, 1734 (1997). (10.1128/jb.179.5.1734-1747.1997) / J. Bacteriol. by Gruber T. M. (1997)
  14. Lonetto M., Gribskov M., Gross C. A., J. Bacteriol. 174, 3843 (1992). (10.1128/jb.174.12.3843-3849.1992) / J. Bacteriol. by Lonetto M. (1992)
  15. 10.1126/science.1059495
  16. N. Korzheva et al. Science 289 619 (2000). (10.1126/science.289.5479.619)
  17. K. Severinov et al. J. Biol. Chem. 269 20826 (1994). (10.1016/S0021-9258(17)31896-3)
  18. Reviewed in S. A. Darst et al. in Nucleic Acids and Molecular Biology F. Ekstein D. M. J. Lilley Eds. (Springer London 1997) vol. 11 pp. 27–40.
  19. Barne K. A., Bown J. A., Busby S. J. W., Minchin S. D., EMBO J. 16, 4034 (1997). (10.1093/emboj/16.13.4034) / EMBO J. by Barne K. A. (1997)
  20. Gardella T., Moyle T., Susskind M. M., J. Mol. Biol. 206, 579 (1989). (10.1016/0022-2836(89)90567-6) / J. Mol. Biol. by Gardella T. (1989)
  21. Siegele D. A., Hu J. C., Walter W. A., Gross C. A., J. Mol. Biol. 206, 591 (1989). (10.1016/0022-2836(89)90568-8) / J. Mol. Biol. by Siegele D. A. (1989)
  22. P. Cramer et al. Science 288 640 (2000). (10.1126/science.288.5466.640)
  23. J. Fu et al. Cell 98 799 (1999). (10.1016/S0092-8674(00)81514-7)
  24. S. A. Darst et al. Proc. Natl. Acad. Sci. U.S.A. 99 4296 (2002). (10.1073/pnas.052054099)
  25. 10.1006/jmbi.1998.2439
  26. Janin J., Miller S., Chothia C., J. Mol. Biol. 204, 155 (1988). (10.1016/0022-2836(88)90606-7) / J. Mol. Biol. by Janin J. (1988)
  27. M. M. Sharp et al. Genes Dev. 13 3015 (1999). (10.1101/gad.13.22.3015)
  28. Arthur T. M., Anthony L. C., Burgess R. R., J. Biol. Chem. 275, 23113 (2000). (10.1074/jbc.M002040200) / J. Biol. Chem. by Arthur T. M. (2000)
  29. B. A. Young et al. Cell 105 935 (2001). (10.1016/S0092-8674(01)00398-1)
  30. Joo D. M., Ng N., Calendar R., Proc. Natl. Acad. Sci. U.S.A. 94, 4907 (1997). (10.1073/pnas.94.10.4907) / Proc. Natl. Acad. Sci. U.S.A. by Joo D. M. (1997)
  31. J. A. Camarero et al. Proc. Natl. Acad. Sci. U.S.A. in press.
  32. Dombroski A. J., Walter W. A., Record M. T., Siegele D. A., Gross C. A., Cell 70, 501 (1992). (10.1016/0092-8674(92)90174-B) / Cell by Dombroski A. J. (1992)
  33. Vuthoori S., Bowers C. W., McCracken A., Dombroski A. J., Hinton D. M., J. Mol. Biol. 309, 561 (2001). (10.1006/jmbi.2001.4690) / J. Mol. Biol. by Vuthoori S. (2001)
  34. Nagai H., Shimamoto N., Genes Cells 2, 725 (1997). (10.1046/j.1365-2443.1997.1600357.x) / Genes Cells by Nagai H. (1997)
  35. 10.1126/science.1069595
  36. Sen R., Nagai H., Hernandez V. J., Shimamoto N., J. Biol. Chem. 273, 9872 (1998). (10.1074/jbc.273.16.9872) / J. Biol. Chem. by Sen R. (1998)
  37. Shimamoto N., Kamigochi T., Utiyama H., J. Biol. Chem. 261, 11859 (1986). (10.1016/S0021-9258(18)67321-1) / J. Biol. Chem. by Shimamoto N. (1986)
  38. Bhargava P., Kassavetis G. A., J. Biol. Chem. 274, 26550 (1999). (10.1074/jbc.274.37.26550) / J. Biol. Chem. by Bhargava P. (1999)
  39. 10.1016/S0021-9258(18)48127-6
  40. 10.1128/mr.57.3.703-724.1993
  41. 10.1002/prot.340110407
  42. 10.1107/S0021889891007240
  43. Z. Otwinowski in Proc. CCP4 Study Weekend W. Wolf P. R. Evans A. G. W. Leslie Eds. (Science and Engineering Research Council Daresbury Laboratory Warrington UK 1991) pp. 80–86.
  44. 10.1073/pnas.94.10.5018
  45. We thank G. Schneider for providing Ta 6 Br 14 T. Gaal and R. Gourse for the −10 con promoter fragment and R. Landick for invaluable discussions. We are indebted to A. Joachimiak S. L. Ginell and N. Duke (Advanced Photon Source Structural Biology Center) and to M. Becker and L. Berman (NSLS X25) for support during data collection. Use of the Argonne National Laboratory Structural Biology Center beamlines at the Advanced Photon Source was supported by the U.S. Department of Energy Office of Biological and Environmental Research under contract W-31-109-ENG-38. K.S.M. was supported by a Norman and Rosita Winston Postdoctoral Fellowship and a Human Frontier Science Program Postdoctoral Fellowship. Supported in part by NIH grants GM53759 and GM61898 (S.A.D.).
Dates
Type When
Created 23 years, 1 month ago (July 27, 2002, 5:54 a.m.)
Deposited 1 year, 7 months ago (Jan. 9, 2024, 11:01 p.m.)
Indexed 1 week, 1 day ago (Aug. 20, 2025, 8:32 a.m.)
Issued 23 years, 3 months ago (May 17, 2002)
Published 23 years, 3 months ago (May 17, 2002)
Published Print 23 years, 3 months ago (May 17, 2002)
Funders 0

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@article{Murakami_2002, title={Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution}, volume={296}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.1069594}, DOI={10.1126/science.1069594}, number={5571}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Murakami, Katsuhiko S. and Masuda, Shoko and Darst, Seth A.}, year={2002}, month=may, pages={1280–1284} }