6p0c - Revision history

OCA at 07:20, 11 October 2023

OCA — Wed, 11 Oct 2023 07:20:32 GMT

←Older revision		Revision as of 07:20, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6p0c' size='340' side='right'caption='[[6p0c]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='6p0c' size='340' side='right'caption='[[6p0c]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p0c]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6P0C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p0c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P0C FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.55Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_ligase_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6p0c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0c OCA], [~~http~~://pdbe.org/6p0c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6p0c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6p0c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0c 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=6p0c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0c OCA], [https://pdbe.org/6p0c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p0c RCSB], [https://www.ebi.ac.uk/pdbsum/6p0c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0c ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DNLI1_HUMAN DNLI1_HUMAN]] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.	+	[https://www.uniprot.org/uniprot/DNLI1_HUMAN DNLI1_HUMAN] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6p0c" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6p0c" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA ligase 3D structures\|DNA ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Riccio, A A~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Schellenberg, M J~~]]	+	[[Category: Riccio AA]]
-	[[Category: ~~Tumbale, P S~~]]	+	[[Category: Schellenberg MJ]]
-	[[Category: ~~Williams, R S~~]]	+	[[Category: Tumbale PS]]
-	[[Category: ~~Adenylation domain]]~~	+	[[Category: Williams RS]]
-	~~[[Category: Dna binding domain]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Ligase-dna complex]]~~	+
-	~~[[Category: Metalloenzyme]]~~	+
-	~~[[Category: Ob fold]]~~	+
-	~~[[Category: Phosphotransferase]]~~	+
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 15:10, 11 December 2019

OCA — Wed, 11 Dec 2019 15:10:47 GMT

←Older revision		Revision as of 15:10, 11 December 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6p0c is ~~ON HOLD until Paper~~ Publication	+	==Human DNA Ligase 1 Bound to an Adenylated, hydroxyl terminated DNA nick in EDTA==
		+	<StructureSection load='6p0c' size='340' side='right'caption='[[6p0c]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6p0c]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P0C FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_ligase_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] </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=6p0c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0c OCA], [http://pdbe.org/6p0c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p0c RCSB], [http://www.ebi.ac.uk/pdbsum/6p0c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0c ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DNLI1_HUMAN DNLI1_HUMAN]] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA ligases catalyze the joining of DNA strands to complete DNA replication, recombination and repair transactions. To protect the integrity of the genome, DNA ligase 1 (LIG1) discriminates against DNA junctions harboring mutagenic 3'-DNA mismatches or oxidative DNA damage, but how such high-fidelity ligation is enforced is unknown. Here, X-ray structures and kinetic analyses of LIG1 complexes with undamaged and oxidatively damaged DNA unveil that LIG1 employs Mg(2+)-reinforced DNA binding to validate DNA base pairing during the adenylyl transfer and nick-sealing ligation reaction steps. Our results support a model whereby LIG1 fidelity is governed by a high-fidelity (HiFi) interface between LIG1, Mg(2+), and the DNA substrate that tunes the enzyme to release pro-mutagenic DNA nicks. In a second tier of protection, LIG1 activity is surveilled by Aprataxin (APTX), which suppresses mutagenic and abortive ligation at sites of oxidative DNA damage.

-	~~Authors~~:	+	Two-tiered enforcement of high-fidelity DNA ligation.,Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS Nat Commun. 2019 Nov 28;10(1):5431. doi: 10.1038/s41467-019-13478-7. PMID:31780661<ref>PMID:31780661</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6p0c" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Riccio, A A]]
		+	[[Category: Schellenberg, M J]]
		+	[[Category: Tumbale, P S]]
		+	[[Category: Williams, R S]]
		+	[[Category: Adenylation domain]]
		+	[[Category: Dna binding domain]]
		+	[[Category: Ligase]]
		+	[[Category: Ligase-dna complex]]
		+	[[Category: Metalloenzyme]]
		+	[[Category: Ob fold]]
		+	[[Category: Phosphotransferase]]
		+	[[Category: Protein-dna complex]]

OCA at 04:32, 29 May 2019

OCA — Wed, 29 May 2019 04:32:38 GMT

←Older revision		Revision as of 04:32, 29 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6p0c is ON HOLD	+	The entry 6p0c is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6p0c" [edit=sysop:move=sysop]

OCA — Wed, 22 May 2019 04:11:58 GMT

Protected "6p0c" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:11, 22 May 2019

OCA: New page: '''Unreleased structure''' The entry 6p0c is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 May 2019 04:11:56 GMT

New page: '''Unreleased structure''' The entry 6p0c is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6p0c is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]