6kij - Revision history

OCA at 10:33, 22 November 2023

OCA — Wed, 22 Nov 2023 10:33:57 GMT

←Older revision		Revision as of 10:33, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6kij' size='340' side='right'caption='[[6kij]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='6kij' size='340' side='right'caption='[[6kij]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kij]] is a 2 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=6KIJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KIJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kij]] 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=6KIJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KIJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'~~>~~GOL</scene>, <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]] 1.58Å</td></tr>
-	<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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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=6kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kij OCA], [~~http~~://pdbe.org/6kij PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kij RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kij PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kij 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=6kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kij OCA], [https://pdbe.org/6kij PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kij RCSB], [https://www.ebi.ac.uk/pdbsum/6kij PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kij 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 ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bao, H]]	+	[[Category: Bao H]]
-	[[Category: Huang, H]]	+	[[Category: Huang H]]
-	[[Category: Wang, N]]	+	[[Category: Wang N]]
-	~~[[Category: Abasic site]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna repair~~]]	+

OCA at 16:35, 22 January 2020

OCA — Wed, 22 Jan 2020 16:35:58 GMT

←Older revision		Revision as of 16:35, 22 January 2020
Line 3:		Line 3:
	<StructureSection load='6kij' size='340' side='right'caption='[[6kij]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='6kij' size='340' side='right'caption='[[6kij]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kij]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KIJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KIJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kij]] is a 2 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=6KIJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KIJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
		+	<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=6kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kij OCA], [http://pdbe.org/6kij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kij RCSB], [http://www.ebi.ac.uk/pdbsum/6kij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kij 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=6kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kij OCA], [http://pdbe.org/6kij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kij RCSB], [http://www.ebi.ac.uk/pdbsum/6kij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kij ProSAT]</span></td></tr>
	</table>		</table>
		+	<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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kij" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bao, H]]		[[Category: Bao, H]]

OCA at 05:52, 7 August 2019

OCA — Wed, 07 Aug 2019 05:52:38 GMT

←Older revision		Revision as of 05:52, 7 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kij is ~~ON HOLD~~	+	==Crystal structure of yedK with ssDNA containing an abasic site==
-		+	<StructureSection load='6kij' size='340' side='right'caption='[[6kij]], [[Resolution\|resolution]] 1.58Å' scene=''>
-	~~Authors~~: ~~Wang~~, N., ~~Bao~~, H., ~~Huang~~, H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6kij]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KIJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KIJ FirstGlance]. <br>
-	~~Description: Crystal structure of yedK with ssDNA containing an abasic site~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6kij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kij OCA], [http://pdbe.org/6kij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kij RCSB], [http://www.ebi.ac.uk/pdbsum/6kij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kij ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bao, H]]		[[Category: Bao, H]]
	[[Category: Huang, H]]		[[Category: Huang, H]]
	[[Category: Wang, N]]		[[Category: Wang, N]]
		+	[[Category: Abasic site]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna repair]]

OCA: Protected "6kij" [edit=sysop:move=sysop]

OCA — Wed, 24 Jul 2019 04:17:44 GMT

Protected "6kij" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:17, 24 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kij is ON HOLD Authors: Wang, N., Bao, H., Huang, H. Description: Crystal structure of yedK with ssDNA containing an abasic site [[Category: Unrel...

OCA — Wed, 24 Jul 2019 04:17:42 GMT

New page: '''Unreleased structure''' The entry 6kij is ON HOLD Authors: Wang, N., Bao, H., Huang, H. Description: Crystal structure of yedK with ssDNA containing an abasic site [[Category: Unrel...

New page

'''Unreleased structure'''

The entry 6kij is ON HOLD

Authors: Wang, N., Bao, H., Huang, H.

Description: Crystal structure of yedK with ssDNA containing an abasic site
[[Category: Unreleased Structures]]
[[Category: Bao, H]]
[[Category: Huang, H]]
[[Category: Wang, N]]