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

Ludovic Sauguet (), Pierre Raia, Ghislaine Henneke and Marc Delarue ()
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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
Ghislaine Henneke: Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes
Marc Delarue: Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528

Nature Communications, 2016, vol. 7, issue 1, 1-12

Abstract: 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.

Date: 2016
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DOI: 10.1038/ncomms12227

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