6y3j - Revision history

OCA at 13:18, 24 January 2024

OCA — Wed, 24 Jan 2024 13:18:45 GMT

←Older revision		Revision as of 13:18, 24 January 2024
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	<StructureSection load='6y3j' size='340' side='right'caption='[[6y3j]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6y3j' size='340' side='right'caption='[[6y3j]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6y3j]] is a 1 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=6Y3J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6Y3J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y3j]] is a 1 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=6Y3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y3J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=APR:ADENOSINE~~-~~5-DIPHOSPHORIBOSE'>APR</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]] 2.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[6y2x\|6y2x]], [[6y22\|6y22~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</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"~~>DTX2, KIAA1528, RNF58 ([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=6y3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y3j OCA], [https://pdbe.org/6y3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y3j RCSB], [https://www.ebi.ac.uk/pdbsum/6y3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y3j ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27]~~ </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6y3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y3j OCA], [~~http~~://pdbe.org/6y3j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6y3j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6y3j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6y3j ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DTX2_HUMAN DTX2_HUMAN]] Regulator of Notch signaling, a signaling pathway involved in cell-cell communications that regulates a broad spectrum of cell-fate determinations. Probably acts both as a positive and negative regulator of Notch, depending on the developmental and cell context. Mediates the antineural activity of Notch, possibly by inhibiting the transcriptional activation mediated by MATCH1. Functions as a ubiquitin ligase protein in vitro, suggesting that it may regulate the Notch pathway via some ubiquitin ligase activity.	+	[https://www.uniprot.org/uniprot/DTX2_HUMAN DTX2_HUMAN] Regulator of Notch signaling, a signaling pathway involved in cell-cell communications that regulates a broad spectrum of cell-fate determinations. Probably acts both as a positive and negative regulator of Notch, depending on the developmental and cell context. Mediates the antineural activity of Notch, possibly by inhibiting the transcriptional activation mediated by MATCH1. Functions as a ubiquitin ligase protein in vitro, suggesting that it may regulate the Notch pathway via some ubiquitin ligase activity.
	<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: RING-type E3 ubiquitin transferase]]~~	+	[[Category: Buetow L]]
-	[[Category: Buetow, L]]	+	[[Category: Gabrielssen M]]
-	[[Category: Gabrielssen, M]]	+	[[Category: Huang DT]]
-	[[Category: Huang~~, D T]]~~	+
-	~~[[Category: E3 ring ligase]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Par-binding]]~~	+
-	~~[[Category: Ubiquitin]]~~	+
-	~~[[Category: Ubiquitination~~]]	+

OCA at 07:47, 30 September 2020

OCA — Wed, 30 Sep 2020 07:47:27 GMT

←Older revision		Revision as of 07:47, 30 September 2020
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	==RING-DTC domains of Deltex 2, bound to ADP-ribose==		==RING-DTC domains of Deltex 2, bound to ADP-ribose==
-	<StructureSection load='6y3j' size='340' side='right'caption='[[6y3j]]' scene=''>	+	<StructureSection load='6y3j' size='340' side='right'caption='[[6y3j]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y3J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y3J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y3j]] is a 1 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=6Y3J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y3J FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y3j OCA], [http://pdbe.org/6y3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y3j RCSB], [http://www.ebi.ac.uk/pdbsum/6y3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y3j ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</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">[[6y2x\|6y2x]], [[6y22\|6y22]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DTX2, KIAA1528, RNF58 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y3j OCA], [http://pdbe.org/6y3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y3j RCSB], [http://www.ebi.ac.uk/pdbsum/6y3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y3j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DTX2_HUMAN DTX2_HUMAN]] Regulator of Notch signaling, a signaling pathway involved in cell-cell communications that regulates a broad spectrum of cell-fate determinations. Probably acts both as a positive and negative regulator of Notch, depending on the developmental and cell context. Mediates the antineural activity of Notch, possibly by inhibiting the transcriptional activation mediated by MATCH1. Functions as a ubiquitin ligase protein in vitro, suggesting that it may regulate the Notch pathway via some ubiquitin ligase activity.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cross-talk between ubiquitination and ADP-ribosylation regulates spatiotemporal recruitment of key players in many signaling pathways. The DELTEX family ubiquitin ligases (DTX1 to DTX4 and DTX3L) are characterized by a RING domain followed by a C-terminal domain (DTC) of hitherto unknown function. Here, we use two label-free mass spectrometry techniques to investigate the interactome and ubiquitinated substrates of human DTX2 and identify a large proportion of proteins associated with the DNA damage repair pathway. We show that DTX2-catalyzed ubiquitination of these interacting proteins requires PARP1/2-mediated ADP-ribosylation and depends on the DTC domain. Using a combination of structural, biochemical, and cell-based techniques, we show that the DTX2 DTC domain harbors an ADP-ribose-binding pocket and recruits poly-ADP-ribose (PAR)-modified proteins for ubiquitination. This PAR-binding property of DTC domain is conserved across the DELTEX family E3s. These findings uncover a new ADP-ribose-binding domain that facilitates PAR-dependent ubiquitination.
		+
		+	DELTEX2 C-terminal domain recognizes and recruits ADP-ribosylated proteins for ubiquitination.,Ahmed SF, Buetow L, Gabrielsen M, Lilla S, Chatrin C, Sibbet GJ, Zanivan S, Huang DT Sci Adv. 2020 Aug 21;6(34). pii: 6/34/eabc0629. doi: 10.1126/sciadv.abc0629., Print 2020 Aug. PMID:32937373<ref>PMID:32937373</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y3j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Buetow L]]	+	[[Category: RING-type E3 ubiquitin transferase]]
-	[[Category: Gabrielssen M]]	+	[[Category: Buetow, L]]
-	[[Category: Huang DT]]	+	[[Category: Gabrielssen, M]]
		+	[[Category: Huang, D T]]
		+	[[Category: E3 ring ligase]]
		+	[[Category: Ligase]]
		+	[[Category: Par-binding]]
		+	[[Category: Ubiquitin]]
		+	[[Category: Ubiquitination]]

OCA at 06:51, 2 September 2020

OCA — Wed, 02 Sep 2020 06:51:47 GMT

←Older revision		Revision as of 06:51, 2 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6y3j is ~~ON HOLD until Paper Publication~~	+	==RING-DTC domains of Deltex 2, bound to ADP-ribose==
-		+	<StructureSection load='6y3j' size='340' side='right'caption='[[6y3j]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y3J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y3J FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y3j OCA], [http://pdbe.org/6y3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y3j RCSB], [http://www.ebi.ac.uk/pdbsum/6y3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y3j ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Buetow L]]
		+	[[Category: Gabrielssen M]]
		+	[[Category: Huang DT]]

OCA at 05:16, 3 June 2020

OCA — Wed, 03 Jun 2020 05:16:54 GMT

←Older revision		Revision as of 05:16, 3 June 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y3j is ON HOLD	+	The entry 6y3j is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 05:00, 27 May 2020

OCA — Wed, 27 May 2020 05:00:46 GMT

←Older revision		Revision as of 05:00, 27 May 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y3j is ON HOLD ~~until Paper Publication~~	+	The entry 6y3j is ON HOLD

	Authors:		Authors:

OCA at 05:43, 4 March 2020

OCA — Wed, 04 Mar 2020 05:43:09 GMT

←Older revision		Revision as of 05:43, 4 March 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y3j is ON HOLD until ~~sometime in the future~~	+	The entry 6y3j is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6y3j" [edit=sysop:move=sysop]

OCA — Wed, 26 Feb 2020 08:19:49 GMT

Protected "6y3j" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:19, 26 February 2020

OCA: New page: '''Unreleased structure''' The entry 6y3j is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Feb 2020 08:19:47 GMT

New page: '''Unreleased structure''' The entry 6y3j is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6y3j is ON HOLD until sometime in the future

Authors:

Description:
[[Category: Unreleased Structures]]