View source for 5uug


==Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (9-mer product complex)==
<StructureSection load='5uug' size='340' side='right'caption='[[5uug]], [[Resolution|resolution]] 1.71&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5uug]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UUG 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]] 1.712&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene>, <scene name='pdbligand=YTA:yatakemycin-adenine+nucleobase+adduct'>YTA</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=5uug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uug OCA], [https://pdbe.org/5uug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uug RCSB], [https://www.ebi.ac.uk/pdbsum/5uug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uug ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q816E8_BACCR Q816E8_BACCR] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Yatakemycin (YTM) is an extraordinarily toxic DNA alkylating agent with potent antimicrobial and antitumor properties and is the most recent addition to the CC-1065 and duocarmycin family of natural products. Though bulky DNA lesions the size of those produced by YTM are normally removed from the genome by the nucleotide-excision repair (NER) pathway, YTM adducts are also a substrate for the bacterial DNA glycosylases AlkD and YtkR2, unexpectedly implicating base-excision repair (BER) in their elimination. The reason for the extreme toxicity of these lesions and the molecular basis for the way they are eliminated by BER have been unclear. Here, we describe the structural and biochemical properties of YTM adducts that are responsible for their toxicity, and define the mechanism by which they are excised by AlkD. These findings delineate an alternative strategy for repair of bulky DNA damage and establish the cellular utility of this pathway relative to that of NER.

Toxicity and repair of DNA adducts produced by the natural product yatakemycin.,Mullins EA, Shi R, Eichman BF Nat Chem Biol. 2017 Jul 24. doi: 10.1038/nchembio.2439. PMID:28759018<ref>PMID:28759018</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5uug" style="background-color:#fffaf0;"></div>

==See Also==
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus cereus]]
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Eichman BF]]
[[Category: Mullins EA]]