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

Type Article
Date 2019-01
Language English
Author(s) Raia PierreORCID1, 2, Carroni MartaORCID3, Henry EtienneORCID5, Pehau-Arnaudet Gerard1, 2, Brule Sebastien1, 2, Beguin Pierre1, Henneke GhislaineORCID4, Lindahl Erik3, Delarue Marc1, 2, Sauguet Ludovic1, 2
Affiliation(s) 1 : Pasteur Inst, Unit Struct Dynam Macromol, Paris, France.
2 : CNRS, UMR 3528, Paris, France.
3 : Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden.
4 : Univ Brest, CNRS, IFREMER, Lab Microbiol Environm Extremes, Plouzane, France.
Source Plos Biology (1545-7885) (Public Library Science), 2019-01 , Vol. 17 , N. 1 , P. e3000122 (28p.)
DOI 10.1371/journal.pbio.3000122
WOS© Times Cited 12
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.

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File Pages Size Access
Publisher's official version 28 7 MB Open access
S1 Table. Values of cryo-EM data collection and 3D reconstruction. 1 175 KB Open access
S2 Table. Data collection and refinement statistics. 1 76 KB Open access
S1 Text. Details on anisotropy and Kd calculations for the DNA-binding assays by steady-state fluorescence anisotropy. 1 178 KB Open access
S2 Text. Details on the structure determination of the DP1 H451A proofreading-deficient variant by X-ray crystallography. 2 84 KB Open access
S1 Fig. FSC curves and local resolutions. 1 176 KB Open access
S2 Fig. Crystal structure of the proofreading-deficient H451A DP1 variant. 1 595 KB Open access
S3 Fig. Purification of the DP1ΔN(144–619)–DP2CTD(1096–1195) complex. 1 115 KB Open access
S4 Fig. Structure-based alignment of the shared structural elements within the catalytic cores of PolD, DNA-dependent RNA polymerases, and RNA-dependent RNA polymerases. 1 241 KB Open access
S5 Fig. Image processing of the cryo-EM 3D reconstruction of PolD. 1 632 KB Open access
S6 Fig. List of rigid-body groups used for real-space refinement. 1 419 KB Open access
S1 Data. 208 KB Open access
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How to cite 

Raia Pierre, Carroni Marta, Henry Etienne, Pehau-Arnaudet Gerard, Brule Sebastien, Beguin Pierre, Henneke Ghislaine, Lindahl Erik, Delarue Marc, Sauguet Ludovic (2019). Structure of the DP1–DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases. Plos Biology, 17(1), e3000122 (28p.). Publisher's official version : https://doi.org/10.1371/journal.pbio.3000122 , Open Access version : https://archimer.ifremer.fr/doc/00477/58883/