6kcz - Revision history

OCA at 10:53, 14 June 2023

2023-06-14T10:53:15Z

←Older revision		Revision as of 10:53, 14 June 2023
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	==Solution structure of the ZnF-UBP domain of USP20/VDU2==		==Solution structure of the ZnF-UBP domain of USP20/VDU2==
-	<StructureSection load='6kcz' size='340' side='right'caption='[[6kcz~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='6kcz' size='340' side='right'caption='[[6kcz]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kcz]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5z4i 5z4i]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KCZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KCZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kcz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5z4i 5z4i]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KCZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KCZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">USP20, KIAA1003, LSFR3A, VDU2 ([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=6kcz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kcz OCA], [https://pdbe.org/6kcz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kcz RCSB], [https://www.ebi.ac.uk/pdbsum/6kcz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kcz 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=6kcz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kcz OCA], [~~http~~://pdbe.org/6kcz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kcz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kcz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kcz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UBP20_HUMAN UBP20_HUMAN]] Deubiquitinating enzyme involved in beta-2 adrenergic receptor (ADRB2) recycling. Acts as a regulator of G-protein coupled receptor (GPCR) signaling by mediating the deubiquitination beta-2 adrenergic receptor (ADRB2). Plays a central role in ADRB2 recycling and resensitization after prolonged agonist stimulation by constitutively binding ADRB2, mediating deubiquitination of ADRB2 and inhibiting lysosomal trafficking of ADRB2. Upon dissociation, it is probably transferred to the translocated beta-arrestins, possibly leading to beta-arrestins deubiquitination and disengagement from ADRB2. This suggests the existence of a dynamic exchange between the ADRB2 and beta-arrestins. Deubiquitinates DIO2, thereby regulating thyroid hormone regulation. Deubiquitinates HIF1A, leading to stabilize HIF1A and enhance HIF1A-mediated activity. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains.<ref>PMID:12056827</ref> <ref>PMID:12865408</ref> <ref>PMID:15776016</ref> <ref>PMID:19424180</ref>	+	[https://www.uniprot.org/uniprot/UBP20_HUMAN UBP20_HUMAN] Deubiquitinating enzyme involved in beta-2 adrenergic receptor (ADRB2) recycling. Acts as a regulator of G-protein coupled receptor (GPCR) signaling by mediating the deubiquitination beta-2 adrenergic receptor (ADRB2). Plays a central role in ADRB2 recycling and resensitization after prolonged agonist stimulation by constitutively binding ADRB2, mediating deubiquitination of ADRB2 and inhibiting lysosomal trafficking of ADRB2. Upon dissociation, it is probably transferred to the translocated beta-arrestins, possibly leading to beta-arrestins deubiquitination and disengagement from ADRB2. This suggests the existence of a dynamic exchange between the ADRB2 and beta-arrestins. Deubiquitinates DIO2, thereby regulating thyroid hormone regulation. Deubiquitinates HIF1A, leading to stabilize HIF1A and enhance HIF1A-mediated activity. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains.<ref>PMID:12056827</ref> <ref>PMID:12865408</ref> <ref>PMID:15776016</ref> <ref>PMID:19424180</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 6kcz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6kcz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[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: Wen Y]]
-	[[Category: Wen, Y]]	+	[[Category: Yang Y]]
-	[[Category: Yang, Y]]	+	[[Category: Zhang N]]
-	[[Category: Zhang, N]]	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 05:44, 21 August 2019

2019-08-21T05:44:37Z

←Older revision		Revision as of 05:44, 21 August 2019
Line 3:		Line 3:
	<StructureSection load='6kcz' size='340' side='right'caption='[[6kcz]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='6kcz' size='340' side='right'caption='[[6kcz]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kcz]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KCZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KCZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kcz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5z4i 5z4i]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KCZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KCZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">USP20, KIAA1003, LSFR3A, VDU2 ([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=6kcz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kcz OCA], [http://pdbe.org/6kcz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kcz RCSB], [http://www.ebi.ac.uk/pdbsum/6kcz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kcz 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=6kcz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kcz OCA], [http://pdbe.org/6kcz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kcz RCSB], [http://www.ebi.ac.uk/pdbsum/6kcz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kcz ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/UBP20_HUMAN UBP20_HUMAN]] Deubiquitinating enzyme involved in beta-2 adrenergic receptor (ADRB2) recycling. Acts as a regulator of G-protein coupled receptor (GPCR) signaling by mediating the deubiquitination beta-2 adrenergic receptor (ADRB2). Plays a central role in ADRB2 recycling and resensitization after prolonged agonist stimulation by constitutively binding ADRB2, mediating deubiquitination of ADRB2 and inhibiting lysosomal trafficking of ADRB2. Upon dissociation, it is probably transferred to the translocated beta-arrestins, possibly leading to beta-arrestins deubiquitination and disengagement from ADRB2. This suggests the existence of a dynamic exchange between the ADRB2 and beta-arrestins. Deubiquitinates DIO2, thereby regulating thyroid hormone regulation. Deubiquitinates HIF1A, leading to stabilize HIF1A and enhance HIF1A-mediated activity. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains.<ref>PMID:12056827</ref> <ref>PMID:12865408</ref> <ref>PMID:15776016</ref> <ref>PMID:19424180</ref>		[[http://www.uniprot.org/uniprot/UBP20_HUMAN UBP20_HUMAN]] Deubiquitinating enzyme involved in beta-2 adrenergic receptor (ADRB2) recycling. Acts as a regulator of G-protein coupled receptor (GPCR) signaling by mediating the deubiquitination beta-2 adrenergic receptor (ADRB2). Plays a central role in ADRB2 recycling and resensitization after prolonged agonist stimulation by constitutively binding ADRB2, mediating deubiquitination of ADRB2 and inhibiting lysosomal trafficking of ADRB2. Upon dissociation, it is probably transferred to the translocated beta-arrestins, possibly leading to beta-arrestins deubiquitination and disengagement from ADRB2. This suggests the existence of a dynamic exchange between the ADRB2 and beta-arrestins. Deubiquitinates DIO2, thereby regulating thyroid hormone regulation. Deubiquitinates HIF1A, leading to stabilize HIF1A and enhance HIF1A-mediated activity. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains.<ref>PMID:12056827</ref> <ref>PMID:12865408</ref> <ref>PMID:15776016</ref> <ref>PMID:19424180</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Deubiquitinase USP20/VDU2 has been demonstrated to play important roles in multiple cellular processes by controlling the life span of substrate proteins including hypoxia-inducible factor HIF1alpha, and so forth. USP20 contains four distinct structural domains including the N-terminal zinc-finger ubiquitin binding domain (ZnF-UBP), the catalytic domain (USP domain), and two tandem DUSP domains, and none of the structures for these four domains has been solved. Meanwhile, except for the ZnF-UBP domain, the biological functions for USP20's catalytic domain and tandem DUSP domains have been at least partially clarified. Here in this study, we determined the solution structure of USP20 ZnF-UBP domain and investigated its binding properties with mono-ubiquitin and poly-ubiquitin (K48-linked di-ubiquitin) by using NMR and molecular modeling techniques. USP20's ZnF-UBP domain forms a spherically shaped fold consisting of a central beta-sheet with either one alpha-helix or two alpha-helices packed on each side of the sheet. However, although having formed a canonical core structure essential for ubiquitin recognition, USP20 ZnF-UBP presents weak ubiquitin binding capacity. The structural basis for understanding USP20 ZnF-UBP's ubiquitin binding capacity was revealed by NMR data-driven docking. Although the electrostatic interactions between D264 of USP5 (E87 in USP20 ZnF-UBP) and R74 of ubiquitin are kept, the loss of the extensive interactions formed between ubiquitin's di-glycine motif and the conserved and non-conserved residues of USP20 ZnF-UBP domain (W41, E55, and Y84) causes a significant decrease in its binding affinity to ubiquitin. Our findings indicate that USP20 ZnF-UBP domain might have a physiological role unrelated to its ubiquitin binding capacity.
		+
		+	Structural and functional studies of USP20 ZnF-UBP domain by NMR.,Yang Y, Ding Y, Zhou C, Wen Y, Zhang N Protein Sci. 2019 Sep;28(9):1606-1619. doi: 10.1002/pro.3675. Epub 2019 Aug 9. PMID:31278784<ref>PMID:31278784</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kcz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ubiquitinyl hydrolase 1]]		[[Category: Ubiquitinyl hydrolase 1]]

OCA at 10:43, 17 July 2019

2019-07-17T10:43:57Z

←Older revision		Revision as of 10:43, 17 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kcz is ~~ON HOLD~~	+	==Solution structure of the ZnF-UBP domain of USP20/VDU2==
-		+	<StructureSection load='6kcz' size='340' side='right'caption='[[6kcz]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~Authors~~: ~~Yang~~, Y., ~~Wen~~, Y., ~~Zhang~~, N.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6kcz]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KCZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KCZ FirstGlance]. <br>
-	~~Description~~: ~~Solution structure~~ of the ~~ZnF~~-~~UBP domain~~ of ~~USP20~~/~~VDU2~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6kcz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kcz OCA], [http://pdbe.org/6kcz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kcz RCSB], [http://www.ebi.ac.uk/pdbsum/6kcz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kcz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UBP20_HUMAN UBP20_HUMAN]] Deubiquitinating enzyme involved in beta-2 adrenergic receptor (ADRB2) recycling. Acts as a regulator of G-protein coupled receptor (GPCR) signaling by mediating the deubiquitination beta-2 adrenergic receptor (ADRB2). Plays a central role in ADRB2 recycling and resensitization after prolonged agonist stimulation by constitutively binding ADRB2, mediating deubiquitination of ADRB2 and inhibiting lysosomal trafficking of ADRB2. Upon dissociation, it is probably transferred to the translocated beta-arrestins, possibly leading to beta-arrestins deubiquitination and disengagement from ADRB2. This suggests the existence of a dynamic exchange between the ADRB2 and beta-arrestins. Deubiquitinates DIO2, thereby regulating thyroid hormone regulation. Deubiquitinates HIF1A, leading to stabilize HIF1A and enhance HIF1A-mediated activity. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains.<ref>PMID:12056827</ref> <ref>PMID:12865408</ref> <ref>PMID:15776016</ref> <ref>PMID:19424180</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ubiquitinyl hydrolase 1]]
	[[Category: Wen, Y]]		[[Category: Wen, Y]]
	[[Category: Yang, Y]]		[[Category: Yang, Y]]
	[[Category: Zhang, N]]		[[Category: Zhang, N]]
		+	[[Category: Hydrolase]]

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

2019-07-10T03:58:55Z

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

←Older revision

Revision as of 03:58, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kcz is ON HOLD Authors: Yang, Y., Wen, Y., Zhang, N. Description: Solution structure of the ZnF-UBP domain of USP20/VDU2 [[Category: Unreleased St...

2019-07-10T03:58:54Z

New page: '''Unreleased structure''' The entry 6kcz is ON HOLD Authors: Yang, Y., Wen, Y., Zhang, N. Description: Solution structure of the ZnF-UBP domain of USP20/VDU2 [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 6kcz is ON HOLD

Authors: Yang, Y., Wen, Y., Zhang, N.

Description: Solution structure of the ZnF-UBP domain of USP20/VDU2
[[Category: Unreleased Structures]]
[[Category: Wen, Y]]
[[Category: Yang, Y]]
[[Category: Zhang, N]]