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Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution

Nature volume 417, pages 712–719 (2002)Cite this article

Abstract

In bacteria, the binding of a single protein, the initiation factor σ, to a multi-subunit RNA polymerase core enzyme results in the formation of a holoenzyme, the active form of RNA polymerase essential for transcription initiation. Here we report the crystal structure of a bacterial RNA polymerase holoenzyme from Thermus thermophilus at 2.6 Å resolution. In the structure, two amino-terminal domains of the σ subunit form a V-shaped structure near the opening of the upstream DNA-binding channel of the active site cleft. The carboxy-terminal domain of σ is near the outlet of the RNA-exit channel, about 57 Å from the N-terminal domains. The extended linker domain forms a hairpin protruding into the active site cleft, then stretching through the RNA-exit channel to connect the N- and C-terminal domains. The holoenzyme structure provides insight into the structural organization of transcription intermediate complexes and into the mechanism of transcription initiation.

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Figure 1: Holoenzyme crystal structure.
Figure 2: Comparison between the holoenzyme and T. aquaticus core structures.
Figure 3: Organization and structure of the σ.
Figure 4: Individual σ domains and their interactions with the core.
Figure 5: Catalytic centre.
Figure 6: Models of the holoenzyme–nucleic acid complexes.

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Acknowledgements

We thank M. Yamamoto for assistance during the data collection at the SPring-8 synchrotron beam line, BL45. We are grateful to T. Yeates for discussions and advice concerning the merohedral twinning problem. This work was supported in part by a grant from the National Institutes of Health to S.B. and by a grant from the Organized Research Combination System of Science and Technology Agency (Japan) to S.Y.

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Authors and Affiliations

  1. Cellular Signaling Laboratory, RIKEN Harima Institute at Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo, 679-5148, Japan

    Dmitry G. Vassylyev, Shun-ichi Sekine & Shigeyuki Yokoyama

  2. Structurome Research Group, RIKEN Harima Institute at Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo, 679-5148, Japan

    Dmitry G. Vassylyev, Shun-ichi Sekine, Marina N. Vassylyeva & Shigeyuki Yokoyama

  3. Department of Microbiology, SUNY Health Science Center, 450 Clarkson Avenue, Brooklyn, New York, 11203, USA

    Oleg Laptenko, Jookyung Lee & Sergei Borukhov

  4. RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, 230-0045, Yokohama, Japan

    Marina N. Vassylyeva & Shigeyuki Yokoyama

  5. Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-0033, Tokyo, Japan

    Shigeyuki Yokoyama

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Correspondence to Dmitry G. Vassylyev.

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Vassylyev, D., Sekine, Si., Laptenko, O. et al. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417, 712–719 (2002). https://doi.org/10.1038/nature752

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