View source for 6nuh


==Non-covalent DNA-protein complex between E. coli YedK and ssDNA containing an abasic site analog==
<StructureSection load='6nuh' size='340' side='right'caption='[[6nuh]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6nuh]] 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=6NUH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NUH 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]] 1.594&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=PDI:PHOSPHORIC+ACID+MONO-(3-HYDROXY-PROPYL)+ESTER'>PDI</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=6nuh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nuh OCA], [https://pdbe.org/6nuh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nuh RCSB], [https://www.ebi.ac.uk/pdbsum/6nuh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nuh ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/YEDK_ECOLI YEDK_ECOLI] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Abasic (AP) sites are one of the most common DNA lesions that block replicative polymerases. 5-hydroxymethylcytosine binding, embryonic stem cell-specific protein (HMCES) recognizes and processes these lesions in the context of single-stranded DNA (ssDNA). A HMCES DNA-protein cross-link (DPC) intermediate is thought to shield the AP site from endonucleases and error-prone polymerases. The highly evolutionarily conserved SOS-response associated peptidase (SRAP) domain of HMCES and its Escherichia coli ortholog YedK mediate lesion recognition. Here we uncover the basis of AP site protection by SRAP domains from a crystal structure of the YedK DPC. YedK forms a stable thiazolidine linkage between a ring-opened AP site and the alpha-amino and sulfhydryl substituents of its amino-terminal cysteine residue. The thiazolidine linkage explains the remarkable stability of the HMCES DPC, its resistance to strand cleavage and the proteolysis requirement for resolution. Furthermore, its structure reveals that HMCES has specificity for AP sites in ssDNA at junctions found when replicative polymerases encounter the AP lesion.

Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link.,Thompson PS, Amidon KM, Mohni KN, Cortez D, Eichman BF Nat Struct Mol Biol. 2019 Jul;26(7):613-618. doi: 10.1038/s41594-019-0255-5. Epub, 2019 Jun 24. PMID:31235915<ref>PMID:31235915</ref>

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