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

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.

Full Text

Publisher's official version
287 Mo
S1 Table. Values of cryo-EM data collection and 3D reconstruction.
1175 Ko
S2 Table. Data collection and refinement statistics.
176 Ko
S1 Text. Details on anisotropy and Kd calculations for the DNA-binding assays by steady-state fluorescence anisotropy.
1178 Ko
S2 Text. Details on the structure determination of the DP1 H451A proofreading-deficient variant by X-ray crystallography.
284 Ko
S1 Fig. FSC curves and local resolutions.
1176 Ko
S2 Fig. Crystal structure of the proofreading-deficient H451A DP1 variant.
1595 Ko
S3 Fig. Purification of the DP1ΔN(144–619)–DP2CTD(1096–1195) complex.
1115 Ko
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.
1241 Ko
S5 Fig. Image processing of the cryo-EM 3D reconstruction of PolD.
1632 Ko
S6 Fig. List of rigid-body groups used for real-space refinement.
1419 Ko
S1 Data.
-208 Ko
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.).,

Copy this text