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Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography

Author

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  • Ludovic Sauguet

    (Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528)

  • Pierre Raia

    (Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528
    Pierre and Marie Curie University, Paris 6)

  • Ghislaine Henneke

    (Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes
    UBO, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes
    CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes)

  • Marc Delarue

    (Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528)

Abstract

Archaeal replicative DNA polymerase D (PolD) constitute an atypical class of DNA polymerases made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2), both with unknown structures. We have determined the crystal structures of Pyrococcus abyssi DP1 and DP2 at 2.5 and 2.2 Å resolution, respectively, revealing a catalytic core strikingly different from all other known DNA polymerases (DNAPs). Rather, the PolD DP2 catalytic core has the same ‘double-psi β-barrel’ architecture seen in the RNA polymerase (RNAP) superfamily, which includes multi-subunit transcriptases of all domains of life, homodimeric RNA-silencing pathway RNAPs and atypical viral RNAPs. This finding bridges together, in non-viral world, DNA transcription and DNA replication within the same protein superfamily. This study documents further the complex evolutionary history of the DNA replication apparatus in different domains of life and proposes a classification of all extant DNAPs.

Suggested Citation

  • Ludovic Sauguet & Pierre Raia & Ghislaine Henneke & Marc Delarue, 2016. "Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography," Nature Communications, Nature, vol. 7(1), pages 1-12, November.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12227
    DOI: 10.1038/ncomms12227
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    Cited by:

    1. Sota Yagi & Shunsuke Tagami, 2024. "An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    2. Leonardo Betancurt-Anzola & Markel Martínez-Carranza & Marc Delarue & Kelly M. Zatopek & Andrew F. Gardner & Ludovic Sauguet, 2023. "Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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