6HMS

Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA

Summary for 6HMS

• Entry DOI: 10.2210/pdb6hms/pdb
• EMDB information: 0244
• Descriptor: DNA polymerase II small subunit, DNA polymerase II large subunit,DNA polymerase II large subunit, DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3'), ... (6 entities in total)
• Functional Keywords: dna, polymerase d, pyrococcus, replication
• Biological source: Pyrococcus abyssi; More
• Total number of polymer chains: 4
• Total formula weight: 199301.59

Authors

Raia, P.,Carroni, M.,Sauguet, L. (deposition date: 2018-09-12, release date: 2019-01-30, Last modification date: 2024-05-15)

Primary citation

Raia, P.,Carroni, M.,Henry, E.,Pehau-Arnaudet, G.,Brule, S.,Beguin, P.,Henneke, G.,Lindahl, E.,Delarue, M.,Sauguet, L.
Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases.
PLoS Biol., 17:e3000122-e3000122, 2019

PubMed Abstract: 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.

PubMed: 30657780
DOI: 10.1371/journal.pbio.3000122

Experimental method

ELECTRON MICROSCOPY (7.1 Å)