View source for 5vhv


==Pseudomonas fluorescens alkylpurine DNA glycosylase AlkC bound to DNA containing an oxocarbenium-intermediate analog==
<StructureSection load='5vhv' size='340' side='right'caption='[[5vhv]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5vhv]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens] 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=5VHV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VHV 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]] 1.799&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9B4:(2R,5R,13R,16R)-9-(hydroxymethyl)-9-{[(2R)-2-hydroxypropoxy]methyl}-5,13-dimethyl-4,7,11,14-tetraoxaheptadecane-2,16-diol'>9B4</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5vhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vhv OCA], [https://pdbe.org/5vhv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vhv RCSB], [https://www.ebi.ac.uk/pdbsum/5vhv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vhv ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/C3K795_PSEFS C3K795_PSEFS] 
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== Publication Abstract from PubMed ==
DNA glycosylases preserve genome integrity and define the specificity of the base excision repair pathway for discreet, detrimental modifications, and thus, the mechanisms by which glycosylases locate DNA damage are of particular interest. Bacterial AlkC and AlkD are specific for cationic alkylated nucleobases and have a distinctive HEAT-like repeat (HLR) fold. AlkD uses a unique non-base-flipping mechanism that enables excision of bulky lesions more commonly associated with nucleotide excision repair. In contrast, AlkC has a much narrower specificity for small lesions, principally N3-methyladenine (3mA). Here, we describe how AlkC selects for and excises 3mA using a non-base-flipping strategy distinct from that of AlkD. A crystal structure resembling a catalytic intermediate complex shows how AlkC uses unique HLR and immunoglobulin-like domains to induce a sharp kink in the DNA, exposing the damaged nucleobase to active site residues that project into the DNA This active site can accommodate and excise N3-methylcytosine (3mC) and N1-methyladenine (1mA), which are also repaired by AlkB-catalyzed oxidative demethylation, providing a potential alternative mechanism for repair of these lesions in bacteria.

Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC.,Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David SS, Rokas A, Eichman BF EMBO J. 2017 Oct 20. pii: e201797833. doi: 10.15252/embj.201797833. PMID:29054852<ref>PMID:29054852</ref>

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

==See Also==
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas fluorescens]]
[[Category: Synthetic construct]]
[[Category: Eichman BF]]
[[Category: Shi R]]