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TitleStructure of eukaryotic DNA polymerase δ bound to the PCNA clamp while encircling DNA.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 117, Issue 48, Page 30344-30353, Year 2020
Publish dateDec 1, 2020
AuthorsFengwei Zheng / Roxana E Georgescu / Huilin Li / Michael E O'Donnell /
PubMed AbstractThe 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 ...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.
External linksProc Natl Acad Sci U S A / PubMed:33203675 / PubMed Central
MethodsEM (single particle)
Resolution3.2 Å
Structure data

22803

7kc0

EMDB-22803: Cryo-EM 3D map of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp
PDB-7kc0: Structure of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

ChemComp-D3T:
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE

ChemComp-ZN:
Unknown entry

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsREPLICATION / Polymerase delta / PCNA / primed DNA / complex

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