View source for 5ihe


==D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease)==
<StructureSection load='5ihe' size='340' side='right'caption='[[5ihe]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ihe]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IHE FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=D5M:2-DEOXYADENOSINE-5-MONOPHOSPHATE'>D5M</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ihe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ihe OCA], [https://pdbe.org/5ihe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ihe RCSB], [https://www.ebi.ac.uk/pdbsum/5ihe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ihe ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DP2S_PYRAB 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).
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== 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<ref>PMID:27548043</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 5ihe" style="background-color:#fffaf0;"></div>

==See Also==
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus abyssi GE5]]
[[Category: De Larue M]]
[[Category: Raia P]]
[[Category: Sauguet L]]