View source for 5nn7


==KSHV uracil-DNA glycosylase, apo form==
<StructureSection load='5nn7' size='340' side='right'caption='[[5nn7]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5nn7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_gammaherpesvirus_8 Human gammaherpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NN7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NN7 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5nn7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nn7 OCA], [https://pdbe.org/5nn7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nn7 RCSB], [https://www.ebi.ac.uk/pdbsum/5nn7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nn7 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/UNG_HHV8P UNG_HHV8P] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or deamination of cytosines. Therefore may reduce deleterious uracil incorporation into the viral genome, particularly in terminally differentiated cells which lack DNA repair enzymes.[HAMAP-Rule:MF_04046]
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== Publication Abstract from PubMed ==
Efficient gamma-herpesvirus lytic phase replication requires a virally encoded UNG-type uracil-DNA glycosylase as a structural element of the viral replisome. Uniquely, gamma-herpesvirus UNGs carry a seven or eight residue insertion of variable sequence in the otherwise highly conserved minor-groove DNA binding loop. In Epstein-Barr Virus [HHV-4] UNG, this motif forms a disc-shaped loop structure of unclear significance. To ascertain the biological role of the loop insertion, we determined the crystal structure of Kaposi's sarcoma-associated herpesvirus [HHV-8] UNG (kUNG) in its product complex with a uracil-containing dsDNA, as well as two structures of kUNG in its apo state. We find the disc-like conformation is conserved, but only when the kUNG DNA-binding cleft is occupied. Surprisingly, kUNG uses this structure to flip the orphaned partner base of the substrate deoxyuridine out of the DNA duplex while retaining canonical UNG deoxyuridine-flipping and catalysis. The orphan base is stably posed in the DNA major groove which, due to DNA backbone manipulation by kUNG, is more open than in other UNG-dsDNA structures. Mutagenesis suggests a model in which the kUNG loop is pinned outside the DNA-binding cleft until DNA docking promotes rigid structuring of the loop and duplex nucleotide flipping, a novel observation for UNGs.

A structurally conserved motif in gamma-herpesvirus uracil-DNA glycosylases elicits duplex nucleotide-flipping.,Earl C, Bagneris C, Zeman K, Cole A, Barrett T, Savva R Nucleic Acids Res. 2018 Mar 27. pii: 4955253. doi: 10.1093/nar/gky217. PMID:29596604<ref>PMID:29596604</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 5nn7" style="background-color:#fffaf0;"></div>

==See Also==
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Human gammaherpesvirus 8]]
[[Category: Large Structures]]
[[Category: Bagneris C]]
[[Category: Barrett T]]
[[Category: Cole AR]]
[[Category: Earl C]]
[[Category: Savva R]]