5IHE

D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease)

Summary for 5IHE

• Entry DOI: 10.2210/pdb5ihe/pdb
• Descriptor: DNA polymerase II small subunit, 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE, FE (III) ION, ... (8 entities in total)
• Functional Keywords: dna polymerase d-family exonuclease, transferase
• Biological source: Pyrococcus abyssi (strain GE5 / Orsay)
• Total number of polymer chains: 2
• Total formula weight: 108434.34

Authors

Sauguet, L.,Raia, P.,De Larue, M. (deposition date: 2016-02-29, release date: 2016-08-31, Last modification date: 2024-05-08)

Primary citation

Sauguet, L.,Raia, P.,Henneke, G.,Delarue, M.
Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.
Nat Commun, 7:12227-12227, 2016

PubMed Abstract: Archaeal replicative DNA polymerase D (PolD) constitute an atypical class of DNA polymerases made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2), both with unknown structures. We have determined the crystal structures of Pyrococcus abyssi DP1 and DP2 at 2.5 and 2.2 Å resolution, respectively, revealing a catalytic core strikingly different from all other known DNA polymerases (DNAPs). Rather, the PolD DP2 catalytic core has the same 'double-psi β-barrel' architecture seen in the RNA polymerase (RNAP) superfamily, which includes multi-subunit transcriptases of all domains of life, homodimeric RNA-silencing pathway RNAPs and atypical viral RNAPs. This finding bridges together, in non-viral world, DNA transcription and DNA replication within the same protein superfamily. This study documents further the complex evolutionary history of the DNA replication apparatus in different domains of life and proposes a classification of all extant DNAPs.

PubMed: 27548043
DOI: 10.1038/ncomms12227

Experimental method

X-RAY DIFFRACTION (2.5 Å)