Structural basis for the increased processivity of D- family DNA polymerases in complex with PCNA

Type Article
Date 2020-03
Language English
Author(s) Madru Clément1, Henneke GhislaineORCID2, Raia Pierre1, 3, Hugonneau-Beaufet Inès1, Pehau-Arnaudet Gérard4, England Patrick5, Lindahl Erik6, 7, Delarue Marc1, Carroni Marta6, Sauguet Ludovic1
Affiliation(s) 1 : Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France
2 : CNRS, Ifremer, Université de Brest, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
3 : Sorbonne Université, École Doctorale Complexité du Vivant (ED515), Paris, France
4 : Utech UBI, Institut Pasteur, CNRS UMR 3528, Paris, France
5 : Molecular Biophysics Platform, C2RT, Institut Pasteur, CNRS UMR 3528, Paris, France
6 : Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
7 : Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
Source Nature Communications (2041-1723) (Nature Publishing Group), 2020-03 , Vol. 11 , N. 1 , P. 12p.
DOI 10.1038/s41467-020-15392-9
WOS© Times Cited 4
Abstract

Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. In Eukarya and Archaea, the processivity of replicative DNAPs is greatly enhanced by its binding to the proliferative cell nuclear antigen (PCNA) that encircles the DNA. We determined the cryo-EM structure of the DNA-bound PolD–PCNA complex from Pyrococcus abyssi at 3.77 Å. Using an integrative structural biology approach — combining cryo-EM, X-ray crystallography, protein–protein interaction measurements, and activity assays — we describe the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA. PolD recruits PCNA via a complex mechanism, which requires two different PIP-boxes. We infer that the second PIP-box, which is shared with the eukaryotic Polα replicative DNAP, plays a dual role in binding either PCNA or primase, and could be a master switch between an initiation and a processive phase during replication.

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Publisher's official version 12 3 MB Open access
Supplementary Movie 1 11 104 MB Open access
Supplementary Information 12 1 MB Open access
Peer Review 2 395 KB Open access
Reporting Summary 1 373 KB Open access
Description of Additional Supplementary Files 1 373 KB Open access
Supplementary Movie 1 163 MB Open access
Source data file 9 MB Open access
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Madru Clément, Henneke Ghislaine, Raia Pierre, Hugonneau-Beaufet Inès, Pehau-Arnaudet Gérard, England Patrick, Lindahl Erik, Delarue Marc, Carroni Marta, Sauguet Ludovic (2020). Structural basis for the increased processivity of D- family DNA polymerases in complex with PCNA. Nature Communications, 11(1), 12p. Publisher's official version : https://doi.org/10.1038/s41467-020-15392-9 , Open Access version : https://archimer.ifremer.fr/doc/00620/73180/