View source for 4yig


==vaccinia virus D4/A20(1-50) in complex with dsDNA containing an abasic site and free uracyl==
<StructureSection load='4yig' size='340' side='right'caption='[[4yig]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4yig]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus_Copenhagen Vaccinia virus Copenhagen] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YIG 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]] 2.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene>, <scene name='pdbligand=URA:URACIL'>URA</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=4yig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yig OCA], [https://pdbe.org/4yig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yig RCSB], [https://www.ebi.ac.uk/pdbsum/4yig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yig 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 ==
Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase catalytic subunit E9 associated with its heterodimeric co-factor A20/D4 required for processive genome synthesis. While A20 has no known enzymatic activity, D4 is an active uracil-DNA glycosylase (UNG) . The presence of a repair enzyme as a component of the viral replication machinery suggest that, for poxviruses, DNA synthesis and base excision repair is coupled. We present the 2.7A crystal structure of the complex formed by D4 and the first 50 amino acids of A20 (D4/A201 50) bound to a 10-mer DNA duplex containing an abasic site resulting from the cleavage of a uracil base. Comparison of the viral complex with its human counterpart revealed major divergences in the contacts between protein and DNA and in the enzyme orientation on the DNA. However, the conformation of the dsDNA within both structures is very similar suggesting a dominant role of the DNA conformation for UNG function. In contrast to human UNG, D4 appears rigid and we do not observe a conformational change upon DNA binding. We also studied the interaction of D4/A201-50 with different DNA oligomers by surface plasmon resonance. D4 binds weakly to non-specific DNA and to uracil containing substrates but binds abasic sites with a Kd &lt; 1.4 muM. This second DNA complex structure of a family I UNG gives new insight into the role of D4 as a co-factor of vaccinia virus DNA polymerase and allows a better understanding of the structural determinants required for UNG action.

Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA.,Burmeister WP, Tarbouriech N, Fender P, Contesto-Richefeu C, Peyrefitte CN, Iseni F J Biol Chem. 2015 Jun 4. pii: jbc.M115.648352. PMID:26045555<ref>PMID:26045555</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 4yig" style="background-color:#fffaf0;"></div>

==See Also==
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Vaccinia virus Copenhagen]]
[[Category: Burmeister WP]]
[[Category: Iseni F]]
[[Category: Tarbouriech N]]