5lru - Revision history

OCA at 18:43, 18 October 2023

OCA — Wed, 18 Oct 2023 18:43:52 GMT

←Older revision		Revision as of 18:43, 18 October 2023
Line 3:		Line 3:
	<StructureSection load='5lru' size='340' side='right'caption='[[5lru]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5lru' size='340' side='right'caption='[[5lru]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lru]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LRU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5LRU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lru]] 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=5LRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LRU FirstGlance]. <br>
-	</td></tr><tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"~~><span class~~=~~'plainlinks'~~>[~~http://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1~~]~~, with EC number [http://www~~.~~brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </span>~~</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]] 2.2Å</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=5lru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lru OCA], [~~http~~://pdbe.org/5lru PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5lru RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5lru PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5lru 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=5lru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lru OCA], [https://pdbe.org/5lru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lru RCSB], [https://www.ebi.ac.uk/pdbsum/5lru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lru ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/OTU7B_HUMAN OTU7B_HUMAN]] Negative regulator of the non-canonical NF-kappa-B pathway that acts by mediating deubiquitination of TRAF3, an inhibitor of the NF-kappa-B pathway, thereby acting as a negative regulator of B-cell responses. In response to non-canonical NF-kappa-B stimuli, deubiquitinates 'Lys-48'-linked polyubiquitin chains of TRAF3, preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappa-B. Negatively regulates mucosal immunity against infections. Mediates deubiquitination of EGFR. Has deubiquitinating activity toward 'Lys-11', 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. In vitro, has preference for 'Lys-11'-linked polyubiquitin chains; however such data are unsure in vivo. Hydrolyzes both linear and branched forms of polyubiquitin.<ref>PMID:11463333</ref> <ref>PMID:12682062</ref> <ref>PMID:18178551</ref> <ref>PMID:20622874</ref> <ref>PMID:22179831</ref> <ref>PMID:23827681</ref>	+	[https://www.uniprot.org/uniprot/OTU7B_HUMAN OTU7B_HUMAN] Negative regulator of the non-canonical NF-kappa-B pathway that acts by mediating deubiquitination of TRAF3, an inhibitor of the NF-kappa-B pathway, thereby acting as a negative regulator of B-cell responses. In response to non-canonical NF-kappa-B stimuli, deubiquitinates 'Lys-48'-linked polyubiquitin chains of TRAF3, preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappa-B. Negatively regulates mucosal immunity against infections. Mediates deubiquitination of EGFR. Has deubiquitinating activity toward 'Lys-11', 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. In vitro, has preference for 'Lys-11'-linked polyubiquitin chains; however such data are unsure in vivo. Hydrolyzes both linear and branched forms of polyubiquitin.<ref>PMID:11463333</ref> <ref>PMID:12682062</ref> <ref>PMID:18178551</ref> <ref>PMID:20622874</ref> <ref>PMID:22179831</ref> <ref>PMID:23827681</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ubiquitinyl hydrolase 1~~]]	+	[[Category: Akutsu M]]
-	[[Category: ~~Akutsu, M~~]]	+	[[Category: Burke JE]]
-	[[Category: ~~Burke, J E~~]]	+	[[Category: El Oualid F]]
-	[[Category: Elliott~~, P R~~]]	+	[[Category: Elliott PR]]
-	[[Category: Freund~~, S M.V~~]]	+	[[Category: Freund SMV]]
-	[[Category: Gersch, M]]	+	[[Category: Gersch M]]
-	[[Category: Geurink~~, P P~~]]	+	[[Category: Geurink PP]]
-	[[Category: Kawasaki, M]]	+	[[Category: Kawasaki M]]
-	[[Category: Komander, D]]	+	[[Category: Komander D]]
-	[[Category: Kulathu, Y]]	+	[[Category: Kulathu Y]]
-	[[Category: Maslen~~, S L~~]]	+	[[Category: Maslen SL]]
-	[[Category: Mevissen~~, T E.T~~]]	+	[[Category: Mevissen TET]]
-	[[Category: Mulder~~, M P.C]]~~	+	[[Category: Mulder MPC]]
-	~~[[Category: Oualid, F El~~]]	+	[[Category: Ovaa H]]
-	[[Category: Ovaa, H]]	+	[[Category: Van Tol BDM]]
-	[[Category: Tol~~, B D.M van]]~~	+
-	~~[[Category: Deubiquitinase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Otu domain]]~~	+
-	~~[[Category: Protease~~]]	+

OCA at 10:48, 12 August 2020

OCA — Wed, 12 Aug 2020 10:48:05 GMT

←Older revision		Revision as of 10:48, 12 August 2020
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	==Structure of Cezanne/OTUD7B OTU domain==		==Structure of Cezanne/OTUD7B OTU domain==
-	<StructureSection load='5lru' size='340' side='right' caption='[[5lru]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5lru' size='340' side='right'caption='[[5lru]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lru]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LRU OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LRU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lru]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LRU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5LRU FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </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=5lru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lru OCA], [http://pdbe.org/5lru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lru RCSB], [http://www.ebi.ac.uk/pdbsum/5lru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lru ProSAT]</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=5lru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lru OCA], [http://pdbe.org/5lru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lru RCSB], [http://www.ebi.ac.uk/pdbsum/5lru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lru ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ubiquitinyl hydrolase 1]]		[[Category: Ubiquitinyl hydrolase 1]]
	[[Category: Akutsu, M]]		[[Category: Akutsu, M]]

OCA at 11:07, 26 October 2016

OCA — Wed, 26 Oct 2016 11:07:04 GMT

←Older revision		Revision as of 11:07, 26 October 2016
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/OTU7B_HUMAN OTU7B_HUMAN]] Negative regulator of the non-canonical NF-kappa-B pathway that acts by mediating deubiquitination of TRAF3, an inhibitor of the NF-kappa-B pathway, thereby acting as a negative regulator of B-cell responses. In response to non-canonical NF-kappa-B stimuli, deubiquitinates 'Lys-48'-linked polyubiquitin chains of TRAF3, preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappa-B. Negatively regulates mucosal immunity against infections. Mediates deubiquitination of EGFR. Has deubiquitinating activity toward 'Lys-11', 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. In vitro, has preference for 'Lys-11'-linked polyubiquitin chains; however such data are unsure in vivo. Hydrolyzes both linear and branched forms of polyubiquitin.<ref>PMID:11463333</ref> <ref>PMID:12682062</ref> <ref>PMID:18178551</ref> <ref>PMID:20622874</ref> <ref>PMID:22179831</ref> <ref>PMID:23827681</ref>		[[http://www.uniprot.org/uniprot/OTU7B_HUMAN OTU7B_HUMAN]] Negative regulator of the non-canonical NF-kappa-B pathway that acts by mediating deubiquitination of TRAF3, an inhibitor of the NF-kappa-B pathway, thereby acting as a negative regulator of B-cell responses. In response to non-canonical NF-kappa-B stimuli, deubiquitinates 'Lys-48'-linked polyubiquitin chains of TRAF3, preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappa-B. Negatively regulates mucosal immunity against infections. Mediates deubiquitination of EGFR. Has deubiquitinating activity toward 'Lys-11', 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. In vitro, has preference for 'Lys-11'-linked polyubiquitin chains; however such data are unsure in vivo. Hydrolyzes both linear and branched forms of polyubiquitin.<ref>PMID:11463333</ref> <ref>PMID:12682062</ref> <ref>PMID:18178551</ref> <ref>PMID:20622874</ref> <ref>PMID:22179831</ref> <ref>PMID:23827681</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The post-translational modification of proteins with polyubiquitin regulates virtually all aspects of cell biology. Eight distinct chain linkage types co-exist in polyubiquitin and are independently regulated in cells. This 'ubiquitin code' determines the fate of the modified protein. Deubiquitinating enzymes of the ovarian tumour (OTU) family regulate cellular signalling by targeting distinct linkage types within polyubiquitin, and understanding their mechanisms of linkage specificity gives fundamental insights into the ubiquitin system. Here we reveal how the deubiquitinase Cezanne (also known as OTUD7B) specifically targets Lys11-linked polyubiquitin. Crystal structures of Cezanne alone and in complex with monoubiquitin and Lys11-linked diubiquitin, in combination with hydrogen-deuterium exchange mass spectrometry, enable us to reconstruct the enzymatic cycle in great detail. An intricate mechanism of ubiquitin-assisted conformational changes activates the enzyme, and while all chain types interact with the enzymatic S1 site, only Lys11-linked chains can bind productively across the active site and stimulate catalytic turnover. Our work highlights the plasticity of deubiquitinases and indicates that new conformational states can occur when a true substrate, such as diubiquitin, is bound at the active site.
		+
		+	Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne.,Mevissen TE, Kulathu Y, Mulder MP, Geurink PP, Maslen SL, Gersch M, Elliott PR, Burke JE, van Tol BD, Akutsu M, El Oualid F, Kawasaki M, Freund SM, Ovaa H, Komander D Nature. 2016 Oct 12;538(7625):402-405. doi: 10.1038/nature19836. PMID:27732584<ref>PMID:27732584</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5lru" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:01, 20 October 2016

OCA — Thu, 20 Oct 2016 01:01:03 GMT

←Older revision		Revision as of 01:01, 20 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5lru is ~~ON HOLD~~	+	==Structure of Cezanne/OTUD7B OTU domain==
-		+	<StructureSection load='5lru' size='340' side='right' caption='[[5lru]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5lru]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LRU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LRU FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </span></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=5lru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lru OCA], [http://pdbe.org/5lru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lru RCSB], [http://www.ebi.ac.uk/pdbsum/5lru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lru ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/OTU7B_HUMAN OTU7B_HUMAN]] Negative regulator of the non-canonical NF-kappa-B pathway that acts by mediating deubiquitination of TRAF3, an inhibitor of the NF-kappa-B pathway, thereby acting as a negative regulator of B-cell responses. In response to non-canonical NF-kappa-B stimuli, deubiquitinates 'Lys-48'-linked polyubiquitin chains of TRAF3, preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappa-B. Negatively regulates mucosal immunity against infections. Mediates deubiquitination of EGFR. Has deubiquitinating activity toward 'Lys-11', 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. In vitro, has preference for 'Lys-11'-linked polyubiquitin chains; however such data are unsure in vivo. Hydrolyzes both linear and branched forms of polyubiquitin.<ref>PMID:11463333</ref> <ref>PMID:12682062</ref> <ref>PMID:18178551</ref> <ref>PMID:20622874</ref> <ref>PMID:22179831</ref> <ref>PMID:23827681</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ubiquitinyl hydrolase 1]]
		+	[[Category: Akutsu, M]]
		+	[[Category: Burke, J E]]
		+	[[Category: Elliott, P R]]
		+	[[Category: Freund, S M.V]]
		+	[[Category: Gersch, M]]
		+	[[Category: Geurink, P P]]
		+	[[Category: Kawasaki, M]]
		+	[[Category: Komander, D]]
		+	[[Category: Kulathu, Y]]
		+	[[Category: Maslen, S L]]
		+	[[Category: Mevissen, T E.T]]
		+	[[Category: Mulder, M P.C]]
		+	[[Category: Oualid, F El]]
		+	[[Category: Ovaa, H]]
		+	[[Category: Tol, B D.M van]]
		+	[[Category: Deubiquitinase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Otu domain]]
		+	[[Category: Protease]]

OCA: Protected "5lru" [edit=sysop:move=sysop]

OCA — Fri, 09 Sep 2016 15:14:58 GMT

Protected "5lru" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:14, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5lru is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Sep 2016 15:14:57 GMT

New page: '''Unreleased structure''' The entry 5lru is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5lru is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]