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Structural basis for transcription inhibition by tagetitoxin

Nature Structural & Molecular Biology volume 12, pages 10861093 (2005) | Download Citation

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Abstract

Tagetitoxin (Tgt) inhibits transcription by an unknown mechanism. A structure at a resolution of 2.4 Å of the Thermus thermophilus RNA polymerase (RNAP)–Tgt complex revealed that the Tgt-binding site within the RNAP secondary channel overlaps that of the stringent control effector ppGpp, which partially protects RNAP from Tgt inhibition. Tgt binding is mediated exclusively through polar interactions with the β and β′ residues whose substitutions confer resistance to Tgt in vitro. Importantly, a Tgt phosphate, together with two active site acidic residues, coordinates the third Mg2+ ion, which is distinct from the two catalytic metal ions. We show that Tgt inhibits all RNAP catalytic reactions and propose a mechanism in which the Tgt-bound Mg2+ ion has a key role in stabilization of an inactive transcription intermediate. Remodeling of the active site by metal ions could be a common theme in the regulation of catalysis by nucleic acid enzymes.

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Acknowledgements

We thank R. Landick and J. Roberts for helpful comments. This work was supported by grants GM74252 and GM74840 (to D.G.V.) and GM67153 (to I.A.) from the US National Institutes of Health, and by RIKEN (D.G.V.).

Author information

Affiliations

  1. Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA.

    • Dmitry G Vassylyev
    • , Marina N Vassylyeva
    •  & Anna Perederina
  2. Structural and Molecular Biology Laboratory, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan.

    • Dmitry G Vassylyev
    • , Marina N Vassylyeva
    •  & Anna Perederina
  3. Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.

    • Vladimir Svetlov
    •  & Irina Artsimovitch
  4. Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.

    • Noriyuki Igarashi
    • , Naohiro Matsugaki
    •  & Soichi Wakatsuki

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The authors declare no competing financial interests.

Corresponding authors

Correspondence to Dmitry G Vassylyev or Irina Artsimovitch.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    Tgt inhibits transcription by the E. coli and T. thermophilus RNAPs similarly

  2. 2.

    Supplementary Fig. 2

    Comparison with the eukaryotic enzymes

  3. 3.

    Supplementary Fig. 3

    Tgt acts as an uncompetitive inhibitor.

  4. 4.

    Supplementary Table 1

    Plasmids and oligonucleotides used in this work

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DOI

https://doi.org/10.1038/nsmb1015

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