6cvo - Revision history

OCA at 15:11, 4 October 2023

2023-10-04T15:11:44Z

←Older revision		Revision as of 15:11, 4 October 2023
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	<StructureSection load='6cvo' size='340' side='right'caption='[[6cvo]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6cvo' size='340' side='right'caption='[[6cvo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cvo]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CVO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CVO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cvo]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CVO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CVO 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=BME:BETA~~-~~MERCAPTOETHANOL'>BME</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[4ndf\|4ndf]]~~<~~/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=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">APTX, AXA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=6cvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cvo OCA], [https://pdbe.org/6cvo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cvo RCSB], [https://www.ebi.ac.uk/pdbsum/6cvo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cvo 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=6cvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cvo OCA], [~~http~~://pdbe.org/6cvo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cvo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cvo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cvo ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/APTX_HUMAN APTX_HUMAN]] Defects in APTX are the cause of ataxia-oculomotor apraxia syndrome (AOA) [MIM:[~~http~~://omim.org/entry/208920 208920]]. AOA is an autosomal recessive syndrome characterized by early-onset cerebellar ataxia, oculomotor apraxia, early areflexia and late peripheral neuropathy.<ref>PMID:11586299</ref> <ref>PMID:11586300</ref> <ref>PMID:12196655</ref> <ref>PMID:12629250</ref> <ref>PMID:14506070</ref> <ref>PMID:15852392</ref> <ref>PMID:15699391</ref>	+	[https://www.uniprot.org/uniprot/APTX_HUMAN APTX_HUMAN] Defects in APTX are the cause of ataxia-oculomotor apraxia syndrome (AOA) [MIM:[https://omim.org/entry/208920 208920]. AOA is an autosomal recessive syndrome characterized by early-onset cerebellar ataxia, oculomotor apraxia, early areflexia and late peripheral neuropathy.<ref>PMID:11586299</ref> <ref>PMID:11586300</ref> <ref>PMID:12196655</ref> <ref>PMID:12629250</ref> <ref>PMID:14506070</ref> <ref>PMID:15852392</ref> <ref>PMID:15699391</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/APTX_HUMAN APTX_HUMAN]] DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair and base excision repair. Resolves abortive DNA ligation intermediates formed either at base excision sites, or when DNA ligases attempt to repair non-ligatable breaks induced by reactive oxygen species. Catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined. Also able to hydrolyze adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity.<ref>PMID:14755728</ref> <ref>PMID:15044383</ref> <ref>PMID:16547001</ref> <ref>PMID:16964241</ref> <ref>PMID:17276982</ref>	+	[https://www.uniprot.org/uniprot/APTX_HUMAN APTX_HUMAN] DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair and base excision repair. Resolves abortive DNA ligation intermediates formed either at base excision sites, or when DNA ligases attempt to repair non-ligatable breaks induced by reactive oxygen species. Catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined. Also able to hydrolyze adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity.<ref>PMID:14755728</ref> <ref>PMID:15044383</ref> <ref>PMID:16547001</ref> <ref>PMID:16964241</ref> <ref>PMID:17276982</ref>
	<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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Schellenberg~~, M J~~]]	+	[[Category: Schellenberg MJ]]
-	[[Category: Tumbale~~, P P~~]]	+	[[Category: Tumbale PP]]
-	[[Category: Williams~~, R S]]~~	+	[[Category: Williams RS]]
-	~~[[Category: 5'-dna end processing]]~~	+
-	~~[[Category: 5'-dna end recognition]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Histidine triad domain]]~~	+
-	~~[[Category: Hit domain]]~~	+
-	~~[[Category: Hydrolase-dna-rna complex]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 09:51, 18 December 2019

2019-12-18T09:51:51Z

←Older revision		Revision as of 09:51, 18 December 2019
Line 1:		Line 1:

	==Human Aprataxin (Aptx) bound to nicked RNA-DNA, AMP and Zn product complex==		==Human Aprataxin (Aptx) bound to nicked RNA-DNA, AMP and Zn product complex==
-	<StructureSection load='6cvo' size='340' side='right' caption='[[6cvo]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='6cvo' size='340' side='right'caption='[[6cvo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6cvo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CVO FirstGlance]. <br>		<table><tr><td colspan='2'>[[6cvo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CVO FirstGlance]. <br>
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Schellenberg, M J]]		[[Category: Schellenberg, M J]]
	[[Category: Tumbale, P P]]		[[Category: Tumbale, P P]]

OCA at 08:34, 21 February 2019

2019-02-21T08:34:51Z

←Older revision		Revision as of 08:34, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='6cvo' size='340' side='right' caption='[[6cvo]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6cvo' size='340' side='right' caption='[[6cvo]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cvo]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CVO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cvo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CVO 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=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</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=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ndf\|4ndf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ndf\|4ndf]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APTX, AXA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6cvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cvo OCA], [http://pdbe.org/6cvo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cvo RCSB], [http://www.ebi.ac.uk/pdbsum/6cvo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cvo 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=6cvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cvo OCA], [http://pdbe.org/6cvo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cvo RCSB], [http://www.ebi.ac.uk/pdbsum/6cvo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cvo ProSAT]</span></td></tr>
	</table>		</table>
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Schellenberg, M J]]		[[Category: Schellenberg, M J]]
	[[Category: Tumbale, P P]]		[[Category: Tumbale, P P]]

OCA at 07:26, 29 August 2018

2018-08-29T07:26:53Z

←Older revision		Revision as of 07:26, 29 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6cvo is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Human Aprataxin (Aptx) bound to nicked RNA-DNA, AMP and Zn product complex==
		+	<StructureSection load='6cvo' size='340' side='right' caption='[[6cvo]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6cvo]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CVO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CVO 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=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ndf\|4ndf]]</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=6cvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cvo OCA], [http://pdbe.org/6cvo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cvo RCSB], [http://www.ebi.ac.uk/pdbsum/6cvo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cvo ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/APTX_HUMAN APTX_HUMAN]] Defects in APTX are the cause of ataxia-oculomotor apraxia syndrome (AOA) [MIM:[http://omim.org/entry/208920 208920]]. AOA is an autosomal recessive syndrome characterized by early-onset cerebellar ataxia, oculomotor apraxia, early areflexia and late peripheral neuropathy.<ref>PMID:11586299</ref> <ref>PMID:11586300</ref> <ref>PMID:12196655</ref> <ref>PMID:12629250</ref> <ref>PMID:14506070</ref> <ref>PMID:15852392</ref> <ref>PMID:15699391</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/APTX_HUMAN APTX_HUMAN]] DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair and base excision repair. Resolves abortive DNA ligation intermediates formed either at base excision sites, or when DNA ligases attempt to repair non-ligatable breaks induced by reactive oxygen species. Catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined. Also able to hydrolyze adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity.<ref>PMID:14755728</ref> <ref>PMID:15044383</ref> <ref>PMID:16547001</ref> <ref>PMID:16964241</ref> <ref>PMID:17276982</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The failure of DNA ligases to complete their catalytic reactions generates cytotoxic adenylated DNA strand breaks. The APTX RNA-DNA deadenylase protects genome integrity and corrects abortive DNA ligation arising during ribonucleotide excision repair and base excision DNA repair, and APTX human mutations cause the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1). How APTX senses cognate DNA nicks and is inactivated in AOA1 remains incompletely defined. Here, we report X-ray structures of APTX engaging nicked RNA-DNA substrates that provide direct evidence for a wedge-pivot-cut strategy for 5'-AMP resolution shared with the alternate 5'-AMP processing enzymes POLbeta and FEN1. Our results uncover a DNA-induced fit mechanism regulating APTX active site loop conformations and assembly of a catalytically competent active center. Further, based on comprehensive biochemical, X-ray and solution NMR results, we define a complex hierarchy for the differential impacts of the AOA1 mutational spectrum on APTX structure and activity. Sixteen AOA1 variants impact APTX protein stability, one mutation directly alters deadenylation reaction chemistry, and a dominant AOA1 variant unexpectedly allosterically modulates APTX active site conformations.

-	~~Authors~~:	+	Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.,Tumbale P, Schellenberg MJ, Mueller GA, Fairweather E, Watson M, Little JN, Krahn J, Waddell I, London RE, Williams RS EMBO J. 2018 Jun 22. pii: embj.201798875. doi: 10.15252/embj.201798875. PMID:29934293<ref>PMID:29934293</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6cvo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Schellenberg, M J]]
		+	[[Category: Tumbale, P P]]
		+	[[Category: Williams, R S]]
		+	[[Category: 5'-dna end processing]]
		+	[[Category: 5'-dna end recognition]]
		+	[[Category: Dna repair]]
		+	[[Category: Histidine triad domain]]
		+	[[Category: Hit domain]]
		+	[[Category: Hydrolase-dna-rna complex]]
		+	[[Category: Protein-dna complex]]
		+	[[Category: Zinc-finger]]

OCA at 04:48, 9 May 2018

2018-05-09T04:48:48Z

←Older revision		Revision as of 04:48, 9 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2018-04-04T04:44:59Z

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

←Older revision

Revision as of 04:44, 4 April 2018

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

2018-04-04T04:44:58Z

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

New page

'''Unreleased structure'''

The entry 6cvo is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]