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| | ==KSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide flipping== | | ==KSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide flipping== |
| - | <StructureSection load='5nnu' size='340' side='right' caption='[[5nnu]], [[Resolution|resolution]] 2.97Å' scene=''> | + | <StructureSection load='5nnu' size='340' side='right'caption='[[5nnu]], [[Resolution|resolution]] 2.97Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5nnu]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-8 Hhv-8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NNU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NNU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5nnu]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_gammaherpesvirus_8 Human gammaherpesvirus 8] 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=5NNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NNU FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.97Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5nnh|5nnh]], [[5nn7|5nn7]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ORF46 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37296 HHV-8])</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=5nnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nnu OCA], [https://pdbe.org/5nnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nnu RCSB], [https://www.ebi.ac.uk/pdbsum/5nnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nnu ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </span></td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5nnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nnu OCA], [http://pdbe.org/5nnu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nnu RCSB], [http://www.ebi.ac.uk/pdbsum/5nnu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nnu ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q76RG8_HHV8 Q76RG8_HHV8]] 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] | + | [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] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[DNA glycosylase|DNA glycosylase]] | + | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Hhv-8]] | + | [[Category: Human gammaherpesvirus 8]] |
| - | [[Category: Uracil-DNA glycosylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Bagneris, C]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Barrett, T]] | + | [[Category: Bagneris C]] |
| - | [[Category: Earl, C]] | + | [[Category: Barrett T]] |
| - | [[Category: Savva, R]] | + | [[Category: Earl C]] |
| - | [[Category: Hydrolase]]
| + | [[Category: Savva R]] |
| - | [[Category: Uracil-dna glycosylase]]
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| Structural highlights
Function
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]
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Earl C, Bagneris C, Zeman K, Cole A, Barrett T, Savva R. A structurally conserved motif in gamma-herpesvirus uracil-DNA glycosylases elicits duplex nucleotide-flipping. Nucleic Acids Res. 2018 Mar 27. pii: 4955253. doi: 10.1093/nar/gky217. PMID:29596604 doi:http://dx.doi.org/10.1093/nar/gky217
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