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

Clément Madru, Ghislaine Henneke, Pierre Raia, Inès Hugonneau-Beaufet, Gérard Pehau-Arnaudet, Patrick England, Erik Lindahl, Marc Delarue, Marta Carroni () and Ludovic Sauguet ()
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Clément Madru: Institut Pasteur and CNRS UMR 3528
Ghislaine Henneke: Université de Brest, Laboratoire de Microbiologie des Environnements Extrêmes
Pierre Raia: Institut Pasteur and CNRS UMR 3528
Inès Hugonneau-Beaufet: Institut Pasteur and CNRS UMR 3528
Gérard Pehau-Arnaudet: Utech UBI, Institut Pasteur, CNRS UMR 3528
Patrick England: Institut Pasteur, CNRS UMR 3528
Erik Lindahl: Stockholm University
Marc Delarue: Institut Pasteur and CNRS UMR 3528
Marta Carroni: Stockholm University
Ludovic Sauguet: Institut Pasteur and CNRS UMR 3528

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-15392-9

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