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3vk8

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Current revision (08:40, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3vk8' size='340' side='right'caption='[[3vk8]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3vk8' size='340' side='right'caption='[[3vk8]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vk8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VK8 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vk8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VK8 FirstGlance]. <br>
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</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></td></tr>
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</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&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CTG:(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5-MONOPHOSPHATE'>CTG</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CTG:(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5-MONOPHOSPHATE'>CTG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a46|3a46]], [[3vk7|3vk7]]</div></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MIMI_L315 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vk8 OCA], [https://pdbe.org/3vk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vk8 RCSB], [https://www.ebi.ac.uk/pdbsum/3vk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vk8 ProSAT]</span></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=3vk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vk8 OCA], [https://pdbe.org/3vk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vk8 RCSB], [https://www.ebi.ac.uk/pdbsum/3vk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vk8 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/FPG_MIMIV FPG_MIMIV]
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Thymine glycol (Tg) and 5-hydroxyuracil (5-OHU) are common oxidized products of pyrimidines, which are recognized and cleaved by two DNA glycosylases of the base excision repair pathway, endonuclease III (Nth) and endonuclease VIII (Nei). Although there are several structures of Nei enzymes unliganded or bound to an abasic (apurinic or apyrimidinic) site, until now there was no structure of an Nei bound to a DNA lesion. Mimivirus Nei1 (MvNei1) is an ortholog of human NEIL1, which was previously crystallized bound to DNA containing an apurinic site (Imamura, K., Wallace, S. S., and Doublie, S. (2009) J. Biol. Chem. 284, 26174-26183). Here, we present two crystal structures of MvNei1 bound to two oxidized pyrimidines, Tg and 5-OHU. Both lesions are flipped out from the DNA helix. Tg is in the anti conformation, whereas 5-OHU adopts both anti and syn conformations in the glycosylase active site. Only two protein side chains (Glu-6 and Tyr-253) are within hydrogen-bonding contact with either damaged base, and mutating these residues did not markedly affect the glycosylase activity. This finding suggests that lesion recognition by Nei occurs before the damaged base flips into the glycosylase active site.
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Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA.,Imamura K, Averill A, Wallace SS, Doublie S J Biol Chem. 2012 Feb 3;287(6):4288-98. Epub 2011 Dec 14. PMID:22170059<ref>PMID:22170059</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3vk8" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Apmv]]
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[[Category: Acanthamoeba polyphaga mimivirus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Averill, A]]
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[[Category: Averill A]]
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[[Category: Doublie, S]]
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[[Category: Doublie S]]
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[[Category: Imamura, K]]
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[[Category: Imamura K]]
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[[Category: Wallace, S S]]
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[[Category: Wallace SS]]
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[[Category: Dna binding]]
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[[Category: Dna glycosylase]]
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[[Category: Dna lesion]]
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[[Category: Hneil1 ortholog]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Thymine glycol]]
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[[Category: Zincless finger]]
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Current revision

Crystal structure of DNA-glycosylase bound to DNA containing Thymine glycol

PDB ID 3vk8

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