5k16 - Revision history

OCA at 19:17, 20 September 2023

2023-09-20T19:17:42Z

←Older revision		Revision as of 19:17, 20 September 2023
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	<StructureSection load='5k16' size='340' side='right'caption='[[5k16]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5k16' size='340' side='right'caption='[[5k16]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k16]] is a 2 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=5K16 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K16 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k16]] is a 2 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=5K16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K16 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=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]] 2.599Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k1c\|5k1c]]~~, [[~~5k1a~~\|~~5k1a]], [[5k1b\|5k1b]], [[5k19\|5k19~~]]</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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>USP12, UBH1, USP12L1 ([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=5k16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k16 OCA], [https://pdbe.org/5k16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k16 RCSB], [https://www.ebi.ac.uk/pdbsum/5k16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k16 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/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=5k16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k16 OCA], [~~http~~://pdbe.org/5k16 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k16 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k16 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k16 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UBP12_HUMAN UBP12_HUMAN]] Deubiquitinating enzyme. Has almost no deubiquitinating activity by itself and requires the interaction with WDR48 to have a high activity. Not involved in deubiquitination of monoubiquitinated FANCD2.<ref>PMID:19075014</ref>	+	[https://www.uniprot.org/uniprot/UBP12_HUMAN UBP12_HUMAN] Deubiquitinating enzyme. Has almost no deubiquitinating activity by itself and requires the interaction with WDR48 to have a high activity. Not involved in deubiquitination of monoubiquitinated FANCD2.<ref>PMID:19075014</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Thioesterase\|Thioesterase]]	+	*[[Thioesterase 3D structures\|Thioesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ubiquitinyl hydrolase 1]]~~	+	[[Category: D'Andrea AD]]
-	~~[[Category:~~ Andrea~~, A D.D~~]]	+	[[Category: Li H]]
-	[[Category: Li, H]]	+	[[Category: Zheng N]]
-	[[Category: Zheng, N]]	+
-	~~[[Category: Deubiquitination]]~~	+
-	~~[[Category: Deubiquitnating enzyme]]~~	+
-	~~[[Category: Dub]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 16:24, 20 November 2019

2019-11-20T16:24:05Z

←Older revision		Revision as of 16:24, 20 November 2019
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	==Crystal structure of free Ubiquitin-specific protease 12==		==Crystal structure of free Ubiquitin-specific protease 12==
-	<StructureSection load='5k16' size='340' side='right' caption='[[5k16]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5k16' size='340' side='right'caption='[[5k16]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k16]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K16 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k16]] is a 2 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=5K16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K16 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=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=GOL:GLYCEROL'>GOL</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">[[5k1c\|5k1c]], [[5k1a\|5k1a]], [[5k1b\|5k1b]], [[5k19\|5k19]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k1c\|5k1c]], [[5k1a\|5k1a]], [[5k1b\|5k1b]], [[5k19\|5k19]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">USP12, UBH1, USP12L1 ([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/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='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=5k16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k16 OCA], [http://pdbe.org/5k16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k16 RCSB], [http://www.ebi.ac.uk/pdbsum/5k16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k16 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=5k16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k16 OCA], [http://pdbe.org/5k16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k16 RCSB], [http://www.ebi.ac.uk/pdbsum/5k16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k16 ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 5k16" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5k16" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thioesterase\|Thioesterase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Ubiquitinyl hydrolase 1]]		[[Category: Ubiquitinyl hydrolase 1]]
	[[Category: Andrea, A D.D]]		[[Category: Andrea, A D.D]]

OCA at 15:19, 26 July 2016

2016-07-26T15:19:12Z

←Older revision		Revision as of 15:19, 26 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k16 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of free Ubiquitin-specific protease 12==
		+	<StructureSection load='5k16' size='340' side='right' caption='[[5k16]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k16]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K16 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=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k1c\|5k1c]], [[5k1a\|5k1a]], [[5k1b\|5k1b]], [[5k19\|5k19]]</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=5k16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k16 OCA], [http://pdbe.org/5k16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k16 RCSB], [http://www.ebi.ac.uk/pdbsum/5k16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k16 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UBP12_HUMAN UBP12_HUMAN]] Deubiquitinating enzyme. Has almost no deubiquitinating activity by itself and requires the interaction with WDR48 to have a high activity. Not involved in deubiquitination of monoubiquitinated FANCD2.<ref>PMID:19075014</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ubiquitin-specific proteases (USPs) constitute the largest family of deubiquitinating enzymes, whose catalytic competency is often modulated by their binding partners through unknown mechanisms. Here we report on a series of crystallographic and biochemical analyses of an evolutionarily conserved deubiquitinase, USP12, which is activated by two beta-propeller proteins, UAF1 and WDR20. Our structures reveal that UAF1 and WDR20 interact with USP12 at two distinct sites far from its catalytic center. Without increasing the substrate affinity of USP12, the two beta-propeller proteins potentiate the enzyme through different allosteric mechanisms. UAF1 docks at the distal end of the USP12 Fingers domain and induces a cascade of structural changes that reach a critical ubiquitin-contacting loop adjacent to the catalytic cleft. By contrast, WDR20 anchors at the base of this loop and remotely modulates the catalytic center of the enzyme. Our results provide a mechanistic example for allosteric activation of USPs by their regulatory partners.

-	~~Authors:~~ Li, H., D'Andrea, A.D., ~~Zheng, N~~.	+	Allosteric Activation of Ubiquitin-Specific Proteases by beta-Propeller Proteins UAF1 and WDR20.,Li H, Lim KS, Kim H, Hinds TR, Jo U, Mao H, Weller CE, Sun J, Chatterjee C, D'Andrea AD, Zheng N Mol Cell. 2016 Jul 21;63(2):249-60. doi: 10.1016/j.molcel.2016.05.031. Epub 2016 , Jun 30. PMID:27373336<ref>PMID:27373336</ref>

-	~~Description: Crystal structure~~ of ~~free Ubiquitin~~-~~specific protease 12~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: D'Andrea, A.D]]	+	<div class="pdbe-citations 5k16" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ubiquitinyl hydrolase 1]]
		+	[[Category: Andrea, A D.D]]
	[[Category: Li, H]]		[[Category: Li, H]]
	[[Category: Zheng, N]]		[[Category: Zheng, N]]
		+	[[Category: Deubiquitination]]
		+	[[Category: Deubiquitnating enzyme]]
		+	[[Category: Dub]]
		+	[[Category: Hydrolase]]

OCA at 13:20, 20 June 2016

2016-06-20T13:20:00Z

←Older revision		Revision as of 13:20, 20 June 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k16 is ON HOLD	+	The entry 5k16 is ON HOLD until Paper Publication

	Authors: Li, H., D'Andrea, A.D., Zheng, N.		Authors: Li, H., D'Andrea, A.D., Zheng, N.

OCA: Protected "5k16" [edit=sysop:move=sysop]

2016-06-01T14:10:33Z

Protected "5k16" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:10, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k16 is ON HOLD Authors: Li, H., D'Andrea, A.D., Zheng, N. Description: Crystal structure of free Ubiquitin-specific protease 12 [[Category: Unrele...

2016-06-01T14:10:31Z

New page: '''Unreleased structure''' The entry 5k16 is ON HOLD Authors: Li, H., D'Andrea, A.D., Zheng, N. Description: Crystal structure of free Ubiquitin-specific protease 12 [[Category: Unrele...

New page

'''Unreleased structure'''

The entry 5k16 is ON HOLD

Authors: Li, H., D'Andrea, A.D., Zheng, N.

Description: Crystal structure of free Ubiquitin-specific protease 12
[[Category: Unreleased Structures]]
[[Category: D'Andrea, A.D]]
[[Category: Li, H]]
[[Category: Zheng, N]]