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Structure paper

TitleStructure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases.
Journal, issue, pagesPLoS Biol, Vol. 17, Issue 1, Page e3000122, Year 2019
Publish dateJan 18, 2019
AuthorsPierre Raia / Marta Carroni / Etienne Henry / Gérard Pehau-Arnaudet / Sébastien Brûlé / Pierre Béguin / Ghislaine Henneke / Erik Lindahl / Marc Delarue / Ludovic Sauguet /
PubMed AbstractPolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal ...PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP). We now report the DNA-bound cryo-electron microscopy (cryo-EM) structure of the heterodimeric DP1-DP2 PolD complex from Pyrococcus abyssi, revealing a unique DNA-binding site. Comparison of PolD and RNAPs extends their structural similarities and brings to light the minimal catalytic core shared by all cellular transcriptases. Finally, elucidating the structure of the PolD DP1-DP2 interface, which is conserved in all eukaryotic replicative DNAPs, clarifies their evolutionary relationships with PolD and sheds light on the domain acquisition and exchange mechanism that occurred during the evolution of the eukaryotic replisome.
External linksPLoS Biol / PubMed:30657780 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.6 - 7.1 Å
Structure data

0244

6hms

EMDB-0244, PDB-6hms:
Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA
Method: EM (single particle) / Resolution: 7.1 Å

PDB-6hmf:
D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease) H451 proof-reading deficient variant
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

Chemicals

ChemComp-FE:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-ACT:
ACETATE ION

ChemComp-CAC:
CACODYLATE ION

ChemComp-CA:
Unknown entry

ChemComp-HOH:
WATER

Source
  • pyrococcus abyssi (archaea)
  • pyrococcus abyssi (strain ge5 / orsay) (archaea)
KeywordsREPLICATION / DNA Polymerase D PolD / DNA / polymerase D / Pyrococcus

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