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TitleCryo-EM structure of apo-form human DNA polymerase δ elucidates its minimal DNA synthesis activity without PCNA.
Journal, issue, pagesJ Biol Chem, Vol. 301, Issue 4, Page 108342, Year 2025
Publish dateFeb 22, 2025
AuthorsYeonoh Shin / Mark Hedglin / Katsuhiko S Murakami /
PubMed AbstractDNA polymerase δ (Pol δ) is a key enzyme in eukaryotic DNA replication and genome maintenance, essential for lagging strand synthesis, leading strand initiation, and DNA repair. While human Pol δ ...DNA polymerase δ (Pol δ) is a key enzyme in eukaryotic DNA replication and genome maintenance, essential for lagging strand synthesis, leading strand initiation, and DNA repair. While human Pol δ exhibits high activity and processivity in its holoenzyme form complexed with proliferating cell nuclear antigen (PCNA), it shows minimal DNA synthesis activity without PCNA, the molecular basis of which remains unclear. Here, we present the cryo-EM structure of the apo-form human Pol δ, comprising the catalytic subunit p125 and regulatory subunits p66, p50, and p12, at an overall resolution of 3.65 Å. We identified an acidic α-helix at the N terminus of p125, which occupies the single-stranded DNA-binding cavity within the polymerase domain in the apo-form Pol δ. This interaction likely inhibits DNA binding in the absence of PCNA, explaining the low activity of apo-form Pol δ. The acidic α-helix is absent in yeast Pol δ, providing a molecular explanation for species-specific differences in PCNA-independent Pol δ activity. These findings provide critical insights into the regulatory mechanisms of Pol δ and its reliance on PCNA for efficient DNA synthesis.
External linksJ Biol Chem / PubMed:39993528 / PubMed Central
MethodsEM (single particle)
Resolution3.65 Å
Structure data

48117

9ekb

EMDB-48117, PDB-9ekb:
Cryo-EM structure of apo-form human DNA polymerase delta
Method: EM (single particle) / Resolution: 3.65 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-SF4:
IRON/SULFUR CLUSTER

Source
  • homo sapiens (human)
KeywordsREPLICATION / DNA polymerase delta / human / cryo-EM

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