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Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution

Nature volume 420, pages 43–50 (2002)Cite this article

Abstract

The single-subunit bacteriophage T7 RNA polymerase carries out the transcription cycle in an identical manner to that of bacterial and eukaryotic multisubunit enzymes. Here we report the crystal structure of a T7 RNA polymerase elongation complex, which shows that incorporation of an 8-base-pair RNA–DNA hybrid into the active site of the enzyme induces a marked rearrangement of the amino-terminal domain. This rearrangement involves alternative folding of about 130 residues and a marked reorientation (about 130° rotation) of a stable core subdomain, resulting in a structure that provides elements required for stable transcription elongation. A wide opening on the enzyme surface that is probably an RNA exit pathway is formed, and the RNA–DNA hybrid is completely buried in a newly formed, deep protein cavity. Binding of 10 base pairs of downstream DNA is stabilized mostly by long-distance electrostatic interactions. The structure implies plausible mechanisms for the various phases of the transcription cycle, and reveals important structural similarities with the multisubunit RNA polymerases.

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Figure 1: The T7 RNAP EC crystal structure.
Figure 2: Comparison between the T7 RNAP EC and IC structures.
Figure 3: Structural homology of the T7 RNAP core subdomain.
Figure 4: Protein–nucleic acid interactions.
Figure 5: Model of the late IC.

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Acknowledgements

We thank Y. Kawano for assistance during the data collection at the SPring-8 synchrotron beam line, BL45. We are grateful to A. Murzin for discussions and advice concerning the analysis of the structure. This work was supported in part by grants from the NIH (USA) (W.T.M.) and the Organized Research Combination System of Science and Technology Agency (Japan) (S.Y.).

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Author notes

  1. Tahir H. Tahirov, Dmitry Temiakov and Shigeyuki Yokoyama: These authors contributed equally to this work

Authors and Affiliations

  1. High Throughput Factory, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo, 679-5148, Japan

    Tahir H. Tahirov

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

    Vsevolod Patlan, Dmitry G. Vassylyev & Shigeyuki Yokoyama

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

    Dmitry G. Vassylyev & Shigeyuki Yokoyama

  4. Morse Institute for Molecular Genetics, Department of Microbiology, SUNY Health Science Center, 450 Clarkson Avenue, Brooklyn, New York, 11203, USA

    Dmitry Temiakov, Michael Anikin & William T. McAllister

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

    Shigeyuki Yokoyama

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

    Shigeyuki Yokoyama

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Correspondence to Dmitry G. Vassylyev or Shigeyuki Yokoyama.

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Tahirov, T., Temiakov, D., Anikin, M. et al. Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution. Nature 420, 43–50 (2002). https://doi.org/10.1038/nature01129

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