View source for 8ppv


==Intermediate conformer of Pyrococcus abyssi DNA polymerase D (PolD) bound to a primer/template substrate containing three consecutive mismatches==
<StructureSection load='8ppv' size='340' side='right'caption='[[8ppv]], [[Resolution|resolution]] 3.02&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8ppv]] is a 7 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=8PPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PPV FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.02&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C7R:2-DEOXY-5-O-THIOPHOSPHONOCYTIDINE'>C7R</scene>, <scene name='pdbligand=GS:GUANOSINE-5-THIO-MONOPHOSPHATE'>GS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PST:THYMIDINE-5-THIOPHOSPHATE'>PST</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=8ppv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ppv OCA], [https://pdbe.org/8ppv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ppv RCSB], [https://www.ebi.ac.uk/pdbsum/8ppv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ppv 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 ==
Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found exclusively in Archaea, contain an unusual RNA polymerase-like catalytic core, and a unique Mre11-like proofreading active site. Here, we present cryo-EM structures of PolD trapped in a proofreading mode, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading. Based on our experimental structures, mutants of PolD were designed and their contribution to mismatch bypass and exonuclease kinetics was determined. This study sheds light on the convergent evolution of structurally distinct families of DNA polymerases, and the domain acquisition and exchange mechanism that occurred during the evolution of the replisome in the three domains of life.

Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases.,Betancurt-Anzola L, Martinez-Carranza M, Delarue M, Zatopek KM, Gardner AF, Sauguet L Nat Commun. 2023 Dec 14;14(1):8306. doi: 10.1038/s41467-023-44125-x. PMID:38097591<ref>PMID:38097591</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8ppv" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus abyssi GE5]]
[[Category: Betancurt-Anzola L]]
[[Category: Gardner AF]]
[[Category: Martinez-Carranza M]]
[[Category: Sauguet L]]
[[Category: Zatopek KM]]