View source for 8qam


==vaccinia virus Uracil DNA glycosidase mutant I197K-V200E-L204K==
<StructureSection load='8qam' size='340' side='right'caption='[[8qam]], [[Resolution|resolution]] 1.32&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8qam]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus_Copenhagen Vaccinia virus Copenhagen]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8QAM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8QAM 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]] 1.32&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=8qam FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8qam OCA], [https://pdbe.org/8qam PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8qam RCSB], [https://www.ebi.ac.uk/pdbsum/8qam PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8qam ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/UNG_VACCC UNG_VACCC] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. Also part of a heterodimeric processivity factor which potentiates the DNA polymerase activity. Binds to DNA (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The year 2022 was marked by the mpox outbreak caused by the human monkeypox virus (MPXV), which is approximately 98% identical to the vaccinia virus (VACV) at the sequence level with regard to the proteins involved in DNA replication. We present the production in the baculovirus-insect cell system of the VACV DNA polymerase holoenzyme, which consists of the E9 polymerase in combination with its co-factor, the A20-D4 heterodimer. This led to the 3.8 A cryo-electron microscopy (cryo-EM) structure of the DNA-free form of the holoenzyme. The model of the holoenzyme was constructed from high-resolution structures of the components of the complex and the A20 structure predicted by AlphaFold 2. The structures do not change in the context of the holoenzyme compared to the previously determined crystal and NMR structures, but the E9 thumb domain became disordered. The E9-A20-D4 structure shows the same compact arrangement with D4 folded back on E9 as observed for the recently solved MPXV holoenzyme structures in the presence and the absence of bound DNA. A conserved interface between E9 and D4 is formed by a cluster of hydrophobic residues. Small-angle X-ray scattering data show that other, more open conformations of E9-A20-D4 without the E9-D4 contact exist in solution using the flexibility of two hinge regions in A20. Biolayer interferometry (BLI) showed that the E9-D4 interaction is indeed weak and transient in the absence of DNA although it is very important, as it has not been possible to obtain viable viruses carrying mutations of key residues within the E9-D4 interface.

Structure and flexibility of the DNA polymerase holoenzyme of vaccinia virus.,Burmeister WP, Boutin L, Balestra AC, Groger H, Ballandras-Colas A, Hutin S, Kraft C, Grimm C, Bottcher B, Fischer U, Tarbouriech N, Iseni F PLoS Pathog. 2024 May 20;20(5):e1011652. doi: 10.1371/journal.ppat.1011652. , eCollection 2024 May. PMID:38768256<ref>PMID:38768256</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8qam" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Vaccinia virus Copenhagen]]
[[Category: Burmeister WP]]
[[Category: Tarbouriech N]]