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Structural basis for transcription elongation by bacterial RNA polymerase

Author

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  • Dmitry G. Vassylyev

    (University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA)

  • Marina N. Vassylyeva

    (University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA)

  • Anna Perederina

    (University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA)

  • Tahir H. Tahirov

    (Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Lied Transplant Center, 10737A, 986805 Nebraska Medical Center, Omaha, Nebraska 68198-7696, USA)

  • Irina Artsimovitch

    (The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA)

Abstract

The RNA polymerase elongation complex (EC) is both highly stable and processive, rapidly extending RNA chains for thousands of nucleotides. Understanding the mechanisms of elongation and its regulation requires detailed information about the structural organization of the EC. Here we report the 2.5-Å resolution structure of the Thermus thermophilus EC; the structure reveals the post-translocated intermediate with the DNA template in the active site available for pairing with the substrate. DNA strand separation occurs one position downstream of the active site, implying that only one substrate at a time can specifically bind to the EC. The upstream edge of the RNA/DNA hybrid stacks on the β′-subunit ‘lid’ loop, whereas the first displaced RNA base is trapped within a protein pocket, suggesting a mechanism for RNA displacement. The RNA is threaded through the RNA exit channel, where it adopts a conformation mimicking that of a single strand within a double helix, providing insight into a mechanism for hairpin-dependent pausing and termination.

Suggested Citation

  • Dmitry G. Vassylyev & Marina N. Vassylyeva & Anna Perederina & Tahir H. Tahirov & Irina Artsimovitch, 2007. "Structural basis for transcription elongation by bacterial RNA polymerase," Nature, Nature, vol. 448(7150), pages 157-162, July.
    • Handle: RePEc:nat:nature:v:448:y:2007:i:7150:d:10.1038_nature05932
    DOI: 10.1038/nature05932
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    Cited by:

    1. Lin-Tai Da & Fátima Pardo Avila & Dong Wang & Xuhui Huang, 2013. "A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase," PLOS Computational Biology, Public Library of Science, vol. 9(4), pages 1-9, April.
    2. Dingwei He & Linlin You & Xiaoxian Wu & Jing Shi & Aijia Wen & Zhi Yan & Wenhui Mu & Chengli Fang & Yu Feng & Yu Zhang, 2022. "Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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