5ity: Difference between revisions

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'''Unreleased structure'''


The entry 5ity is ON HOLD  until Paper Publication
==Crystal Structure of Human NEIL1(P2G) bound to duplex DNA containing Thymine Glycol==
<StructureSection load='5ity' size='340' side='right'caption='[[5ity]], [[Resolution|resolution]] 2.48&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ity]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ITY 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]] 2.48&#8491;</td></tr>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ity FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ity OCA], [https://pdbe.org/5ity PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ity RCSB], [https://www.ebi.ac.uk/pdbsum/5ity PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ity ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NEIL1_HUMAN NEIL1_HUMAN] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized pyrimidines, such as thymine glycol, formamidopyrimidine (Fapy) and 5-hydroxyuracil. Has marginal activity towards 8-oxoguanine. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Has DNA glycosylase/lyase activity towards mismatched uracil and thymine, in particular in U:C and T:C mismatches.<ref>PMID:12200441</ref> <ref>PMID:12509226</ref> <ref>PMID:11904416</ref> <ref>PMID:14522990</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
NEIL1 (Nei-like 1) is a DNA repair glycosylase guarding the mammalian genome against oxidized DNA bases. As the first enzymes in the base-excision repair pathway, glycosylases must recognize the cognate substrates and catalyze their excision. Here we present crystal structures of human NEIL1 bound to a range of duplex DNA. Together with computational and biochemical analyses, our results suggest that NEIL1 promotes tautomerization of thymine glycol (Tg)-a preferred substrate-for optimal binding in its active site. Moreover, this tautomerization event also facilitates NEIL1-catalyzed Tg excision. To our knowledge, the present example represents the first documented case of enzyme-promoted tautomerization for efficient substrate recognition and catalysis in an enzyme-catalyzed reaction.


Authors: Zhu, C., Lu, L., Zhang, J., Yue, Z., Song, J., Zong, S., Liu, M., Stovicek, O., Gao, Y., Yi, C.
Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair.,Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M, Stovicek O, Gao YQ, Yi C Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):7792-7. doi:, 10.1073/pnas.1604591113. Epub 2016 Jun 27. PMID:27354518<ref>PMID:27354518</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Liu, M]]
<div class="pdbe-citations 5ity" style="background-color:#fffaf0;"></div>
[[Category: Zhu, C]]
 
[[Category: Zhang, J]]
==See Also==
[[Category: Stovicek, O]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
[[Category: Gao, Y]]
== References ==
[[Category: Lu, L]]
<references/>
[[Category: Yi, C]]
__TOC__
[[Category: Song, J]]
</StructureSection>
[[Category: Yue, Z]]
[[Category: Homo sapiens]]
[[Category: Zong, S]]
[[Category: Large Structures]]
[[Category: Unidentified]]
[[Category: Gao Y]]
[[Category: Liu M]]
[[Category: Lu L]]
[[Category: Song J]]
[[Category: Stovicek O]]
[[Category: Yi C]]
[[Category: Yue Z]]
[[Category: Zhang J]]
[[Category: Zhu C]]
[[Category: Zong S]]
Retrieved from "https://proteopedia.org/5ity"