6kbz

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<StructureSection load='6kbz' size='340' side='right'caption='[[6kbz]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
<StructureSection load='6kbz' size='340' side='right'caption='[[6kbz]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6kbz]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KBZ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6kbz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KBZ FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yedK, C4J69_22885, ECTO6_01993, EFV06_12905, EFV16_12155, SAMEA3472108_01185, SAMEA3752559_04370 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6kbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kbz OCA], [http://pdbe.org/6kbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kbz RCSB], [http://www.ebi.ac.uk/pdbsum/6kbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kbz ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6kbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kbz OCA], [http://pdbe.org/6kbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kbz RCSB], [http://www.ebi.ac.uk/pdbsum/6kbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kbz ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6kbz" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus coli migula 1895]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bao, H]]
[[Category: Bao, H]]

Revision as of 16:35, 22 January 2020

Crystal structure of yedK with ssDNA containing a tetrahydrofuran abasic site

PDB ID 6kbz

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