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Structure paper

TitleCryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme.
Journal, issue, pagesNat Struct Mol Biol, Vol. 26, Issue 10, Page 955-962, Year 2019
Publish dateOct 3, 2019
AuthorsRinku Jain / William J Rice / Radhika Malik / Robert E Johnson / Louise Prakash / Satya Prakash / Iban Ubarretxena-Belandia / Aneel K Aggarwal /
PubMed AbstractDNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. ...DNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. Saccharomyces cerevisiae Polδ consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 Å) cryo-EM structure of yeast Polδ holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe-4S cluster and emerges as the keystone of Polδ assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Polδ architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.
External linksNat Struct Mol Biol / PubMed:31582849 / PubMed Central
MethodsEM (single particle)
Resolution3.2 Å
Structure data

20235

6p1h

EMDB-20235: Structure of a complex
PDB-6p1h: Cryo-EM Structure of DNA Polymerase Delta Holoenzyme
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

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

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate

ChemComp-CA:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • synthetic construct (others)
Keywordsdna binding protein/dna / DNA binding / enzyme / catalysis / regulation / DNA BINDING PROTEIN / dna binding protein-dna complex

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