7KC0

Structure of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp

Summary for 7KC0

• Entry DOI: 10.2210/pdb7kc0/pdb
• EMDB information: 22803
• Descriptor: DNA (5'-D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3'), ZINC ION, DNA (25-MER), ... (10 entities in total)
• Functional Keywords: polymerase delta, pcna, primed dna, complex, replication
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Total number of polymer chains: 8
• Total formula weight: 327561.27

Authors

Zheng, F.,Georgescu, R.,Li, H.,O'Donnell, M.E. (deposition date: 2020-10-04, release date: 2020-12-02, Last modification date: 2025-05-21)

Primary citation

Zheng, F.,Georgescu, R.E.,Li, H.,O'Donnell, M.E.
Structure of eukaryotic DNA polymerase delta bound to the PCNA clamp while encircling DNA.
Proc.Natl.Acad.Sci.USA, 117:30344-30353, 2020

PubMed Abstract: The DNA polymerase (Pol) δ of (S.c.) is composed of the catalytic subunit Pol3 along with two regulatory subunits, Pol31 and Pol32. Pol δ binds to proliferating cell nuclear antigen (PCNA) and functions in genome replication, repair, and recombination. Unique among DNA polymerases, the Pol3 catalytic subunit contains a 4Fe-4S cluster that may sense the cellular redox state. Here we report the 3.2-Å cryo-EM structure of S.c. Pol δ in complex with primed DNA, an incoming ddTTP, and the PCNA clamp. Unexpectedly, Pol δ binds only one subunit of the PCNA trimer. This singular yet extensive interaction holds DNA such that the 2-nm-wide DNA threads through the center of the 3-nm interior channel of the clamp without directly contacting the protein. Thus, a water-mediated clamp and DNA interface enables the PCNA clamp to "waterskate" along the duplex with minimum drag. Pol31 and Pol32 are positioned off to the side of the catalytic Pol3-PCNA-DNA axis. We show here that Pol31-Pol32 binds single-stranded DNA that we propose underlies polymerase recycling during lagging strand synthesis, in analogy to replicase. Interestingly, the 4Fe-4S cluster in the C-terminal CysB domain of Pol3 forms the central interface to Pol31-Pol32, and this strategic location may explain the regulation of the oxidation state on Pol δ activity, possibly useful during cellular oxidative stress. Importantly, human cancer and other disease mutations map to nearly every domain of Pol3, suggesting that all aspects of Pol δ replication are important to human health and disease.

PubMed: 33203675
DOI: 10.1073/pnas.2017637117

Experimental method

ELECTRON MICROSCOPY (3.2 Å)