View source for 6kbx


==Crystal structure of yedK in complex with ssDNA containing abasic site==
<StructureSection load='6kbx' size='340' side='right'caption='[[6kbx]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6kbx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KBX 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]] 1.221&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</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=6kbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kbx OCA], [https://pdbe.org/6kbx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kbx RCSB], [https://www.ebi.ac.uk/pdbsum/6kbx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kbx ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/YEDK_ECOLI YEDK_ECOLI] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
HMCES and yedK were recently identified as sensors of abasic sites in ssDNA. In this study, we present multiple crystal structures captured in the apo-, nonspecific-substrate-binding, specific-substrate-binding, and product-binding states of yedK. In combination with biochemical data, we unveil the molecular basis of AP site sensing in ssDNA by yedK. Our results indicate that yedK has a strong preference for AP site-containing ssDNA over native ssDNA and that the conserved Glu105 residue is important for identifying AP sites in ssDNA. Moreover, our results reveal that a thiazolidine linkage is formed between yedK and AP sites in ssDNA, with the residues that stabilize the thiazolidine linkage important for the formation of DNA-protein crosslinks between yedK and the AP sites. We propose that our findings offer a unique platform to develop yedK and other SRAP domain-containing proteins as tools for detecting abasic sites in vitro and in vivo.

Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.,Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang H Nucleic Acids Res. 2019 Nov 4;47(19):10388-10399. doi: 10.1093/nar/gkz744. PMID:31504793<ref>PMID:31504793</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6kbx" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Bao H]]
[[Category: Huang H]]
[[Category: Wang N]]