5ihe

From Proteopedia

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

PDB ID 5ihe

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Structural highlights

5ihe is a 2 chain structure with sequence from Pyrococcus abyssi GE5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DP2S_PYRAB Possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3' to 5' direction. Has a template-primer preference which is characteristic of a replicative DNA polymerase (By similarity).

Publication Abstract from PubMed

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 A 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 beta-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.

Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.,Sauguet L, Raia P, Henneke G, Delarue M Nat Commun. 2016 Aug 22;7:12227. doi: 10.1038/ncomms12227. PMID:27548043^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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. 2016 Aug 22;7:12227. doi: 10.1038/ncomms12227. PMID:27548043 doi:http://dx.doi.org/10.1038/ncomms12227