3vk7

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[[Image:3vk7.jpg|left|200px]]
 
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==Crystal structure of DNA-glycosylase bound to DNA containing 5-Hydroxyuracil==
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The line below this paragraph, containing "STRUCTURE_3vk7", creates the "Structure Box" on the page.
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<StructureSection load='3vk7' size='340' side='right'caption='[[3vk7]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3vk7]] 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=3VK7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VK7 FirstGlance]. <br>
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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]] 2.1&#8491;</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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=OHU:2-DEOXY-5-HYDROXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>OHU</scene></td></tr>
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{{STRUCTURE_3vk7| PDB=3vk7 | SCENE= }}
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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=3vk7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vk7 OCA], [https://pdbe.org/3vk7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vk7 RCSB], [https://www.ebi.ac.uk/pdbsum/3vk7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vk7 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/FPG_MIMIV FPG_MIMIV]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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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===Crystal structure of DNA-glycosylase bound to DNA containing 5-Hydroxyuracil===
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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 3vk7" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19625256}}, adds the Publication Abstract to the page
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19625256 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19625256}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[3vk7]] is a 6 chain structure with sequence from [http://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=3VK7 OCA].
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==Reference==
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<ref group="xtra">PMID:019625256</ref><references group="xtra"/>
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[[Category: Acanthamoeba polyphaga mimivirus]]
[[Category: Acanthamoeba polyphaga mimivirus]]
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[[Category: Averill, A.]]
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[[Category: Large Structures]]
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[[Category: Doublie, S.]]
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[[Category: Averill A]]
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[[Category: Imamura, K.]]
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[[Category: Doublie S]]
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[[Category: Wallace, S S.]]
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[[Category: Imamura K]]
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[[Category: 5-hydroxyuracil]]
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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: Zincless finger]]
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Current revision

Crystal structure of DNA-glycosylase bound to DNA containing 5-Hydroxyuracil

PDB ID 3vk7

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