View source for 6ajp


==Complex form of Uracil DNA glycosylase X and deoxyuridine monophosphate.==
<StructureSection load='6ajp' size='340' side='right'caption='[[6ajp]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6ajp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AJP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AJP 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]] 1.334&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</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=6ajp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ajp OCA], [https://pdbe.org/6ajp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ajp RCSB], [https://www.ebi.ac.uk/pdbsum/6ajp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ajp ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A0QP43_MYCS2 A0QP43_MYCS2] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Uracil DNA glycosylases (UDGs) are important DNA repair enzymes that excise uracil from DNA, yielding an abasic site. Recently, UdgX, an unconventional UDG with extremely tight binding to DNA containing uracil, was discovered. The structure of UdgX from Mycobacterium smegmatis in complex with DNA shows an overall similarity to that of family 4 UDGs except for a protruding loop at the entrance of the uracil-binding pocket. Surprisingly, H109 in the loop was found to make a covalent bond to the abasic site to form a stable intermediate, while the excised uracil remained in the pocket of the active site. H109 functions as a nucleophile to attack the oxocarbenium ion, substituting for the catalytic water molecule found in other UDGs. To our knowledge, this change from a catalytic water attack to a direct nucleophilic attack by the histidine residue is unprecedented. UdgX utilizes a unique mechanism of protecting cytotoxic abasic sites from exposure to the cellular environment.

Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision.,Ahn WC, Aroli S, Kim JH, Moon JH, Lee GS, Lee MH, Sang PB, Oh BH, Varshney U, Woo EJ Nat Chem Biol. 2019 Jun;15(6):607-614. doi: 10.1038/s41589-019-0289-3. Epub 2019 , May 17. PMID:31101917<ref>PMID:31101917</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6ajp" style="background-color:#fffaf0;"></div>

==See Also==
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mycolicibacterium smegmatis MC2 155]]
[[Category: Ahn WC]]
[[Category: Aroli S]]
[[Category: Varshney U]]
[[Category: Woo EJ]]