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| | <StructureSection load='6nua' size='340' side='right'caption='[[6nua]], [[Resolution|resolution]] 1.64Å' scene=''> | | <StructureSection load='6nua' size='340' side='right'caption='[[6nua]], [[Resolution|resolution]] 1.64Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6nua]] is a 4 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=6NUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NUA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6nua]] is a 4 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=6NUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NUA FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.64Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yedK, yedG, b1931, JW1916 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6nua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nua OCA], [http://pdbe.org/6nua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nua RCSB], [http://www.ebi.ac.uk/pdbsum/6nua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nua ProSAT]</span></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=6nua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nua OCA], [https://pdbe.org/6nua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nua RCSB], [https://www.ebi.ac.uk/pdbsum/6nua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nua ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/YEDK_ECOLI YEDK_ECOLI] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Amidon, K M]] | + | [[Category: Amidon KM]] |
| - | [[Category: Eichman, B F]] | + | [[Category: Eichman BF]] |
| - | [[Category: Abasic site]]
| + | |
| - | [[Category: Dna binding protein]]
| + | |
| - | [[Category: Dna binding protein-dna complex]]
| + | |
| - | [[Category: Dna-protein crosslink]]
| + | |
| - | [[Category: Replication stress]]
| + | |
| - | [[Category: Thiazolidine]]
| + | |
| Structural highlights
Function
YEDK_ECOLI
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Thompson PS, Amidon KM, Mohni KN, Cortez D, Eichman BF. Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link. Nat Struct Mol Biol. 2019 Jul;26(7):613-618. doi: 10.1038/s41594-019-0255-5. Epub, 2019 Jun 24. PMID:31235915 doi:http://dx.doi.org/10.1038/s41594-019-0255-5
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