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| | ==Crystal structure of DNA-glycosylase bound to DNA containing 5-Hydroxyuracil== | | ==Crystal structure of DNA-glycosylase bound to DNA containing 5-Hydroxyuracil== |
| - | <StructureSection load='3vk7' size='340' side='right' caption='[[3vk7]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='3vk7' size='340' side='right'caption='[[3vk7]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3vk7]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Apmv Apmv]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VK7 FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 2.1Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OHU:2-DEOXY-5-HYDROXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>OHU</scene></td></tr> | + | <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> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a46|3a46]], [[3vk8|3vk8]]</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=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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MIMI_L315 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vk7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vk7 OCA], [http://pdbe.org/3vk7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vk7 RCSB], [http://www.ebi.ac.uk/pdbsum/3vk7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vk7 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/FPG_MIMIV FPG_MIMIV] |
| | <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: Apmv]] | + | [[Category: Acanthamoeba polyphaga mimivirus]] |
| - | [[Category: Averill, A]] | + | [[Category: Large Structures]] |
| - | [[Category: Doublie, S]] | + | [[Category: Averill A]] |
| - | [[Category: Imamura, K]] | + | [[Category: Doublie S]] |
| - | [[Category: Wallace, S S]]
| + | [[Category: Imamura K]] |
| - | [[Category: 5-hydroxyuracil]] | + | [[Category: Wallace SS]] |
| - | [[Category: Dna binding]] | + | |
| - | [[Category: Dna glycosylase]]
| + | |
| - | [[Category: Dna lesion]]
| + | |
| - | [[Category: Hneil1 ortholog]]
| + | |
| - | [[Category: Hydrolase-dna complex]]
| + | |
| - | [[Category: Zincless finger]]
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| Structural highlights
Function
FPG_MIMIV
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Imamura K, Averill A, Wallace SS, Doublie S. Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA. J Biol Chem. 2012 Feb 3;287(6):4288-98. Epub 2011 Dec 14. PMID:22170059 doi:http://dx.doi.org/10.1074/jbc.M111.315309
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