View source for 5kub


==Bacillus cereus DNA glycosylase AlkD bound to 7-methylguanine nucleobase and DNA containing an oxocarbenium-intermediate analog==
<StructureSection load='5kub' size='340' side='right'caption='[[5kub]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5kub]] 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=5KUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KUB 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]] 1.73&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MY6:2-AMINO-7-METHYL-1,7-DIHYDRO-6H-PURIN-6-ONE'>MY6</scene>, <scene name='pdbligand=NRI:PHOSPHORIC+ACID+MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)+ESTER'>NRI</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=5kub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kub OCA], [https://pdbe.org/5kub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kub RCSB], [https://www.ebi.ac.uk/pdbsum/5kub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kub ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q816E8_BACCR Q816E8_BACCR] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA glycosylases protect genomic integrity by locating and excising aberrant nucleobases. Substrate recognition and excision usually take place in an extrahelical conformation, which is often stabilized by pi-stacking interactions between the lesion nucleobase and aromatic side chains in the glycosylase active site. Bacillus cereus AlkD is the only DNA glycosylase known to catalyze base excision without extruding the damaged nucleotide from the DNA helix. Instead of contacting the nucleobase itself, the AlkD active site interacts with the lesion deoxyribose through a series of C-H/pi interactions. These interactions are ubiquitous in protein structures, but evidence for their catalytic significance in enzymology is lacking. Here, we show that the C-H/pi interactions between AlkD and the lesion deoxyribose participate in catalysis of glycosidic bond cleavage. This is the first demonstration of a catalytic role for C-H/pi interactions as intermolecular forces important to DNA repair.

A Catalytic Role for C-H/pi Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD.,Parsons ZD, Bland JM, Mullins EA, Eichman BF J Am Chem Soc. 2016 Sep 1. PMID:27571247<ref>PMID:27571247</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5kub" 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]]