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PLoS Biol. 2019 Jan 18;17(1):e3000122. doi: 10.1371/journal.pbio.3000122. eCollection 2019 Jan.

Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases.

Author information

1
Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, Paris, France.
2
Sorbonne Université, Ecole Doctorale Complexité du Vivant (ED515), Paris, France.
3
Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Sweden.
4
CNRS, IFREMER, Univ Brest, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France.
5
Utech UBI, Pasteur Institute and CNRS UMR 3528, Paris, France.
6
Molecular Biophysics Platform, Pasteur Institute, C2RT and CNRS UMR 3528, Paris, France.
7
Unit of Molecular Biology of Gene in Extremophiles, Pasteur Institute, Paris, France.
8
IFREMER, CNRS, Univ Brest, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France.

Abstract

PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP). We now report the DNA-bound cryo-electron microscopy (cryo-EM) structure of the heterodimeric DP1-DP2 PolD complex from Pyrococcus abyssi, revealing a unique DNA-binding site. Comparison of PolD and RNAPs extends their structural similarities and brings to light the minimal catalytic core shared by all cellular transcriptases. Finally, elucidating the structure of the PolD DP1-DP2 interface, which is conserved in all eukaryotic replicative DNAPs, clarifies their evolutionary relationships with PolD and sheds light on the domain acquisition and exchange mechanism that occurred during the evolution of the eukaryotic replisome.

Conflict of interest statement

The authors have declared that no competing interests exist.

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