6dxt - Revision history

OCA at 07:54, 17 October 2024

2024-10-17T07:54:01Z

← Older revision		Revision as of 07:54, 17 October 2024
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	<table><tr><td colspan='2'>[[6dxt]] 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=6DXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DXT FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dxt]] 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=6DXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DXT FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.95Å</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]] 1.95Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHY:3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic+acid'>HHY~~</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX~~</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHY:3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic+acid'>HHY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6dxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxt OCA], [https://pdbe.org/6dxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dxt RCSB], [https://www.ebi.ac.uk/pdbsum/6dxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxt 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=6dxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxt OCA], [https://pdbe.org/6dxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dxt RCSB], [https://www.ebi.ac.uk/pdbsum/6dxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxt ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[https://www.uniprot.org/uniprot/UBP5_HUMAN UBP5_HUMAN] Cleaves linear and branched multiubiquitin polymers with a marked preference for branched polymers. Involved in unanchored 'Lys-48'-linked polyubiquitin disassembly. Binds linear and 'Lys-63'-linked polyubiquitin with a lower affinity. Knock-down of USP5 causes the accumulation of p53/TP53 and an increase in p53/TP53 transcriptional activity because the unanchored polyubiquitin that accumulates is able to compete with ubiquitinated p53/TP53 but not with MDM2 for proteasomal recognition.<ref>PMID:19098288</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 06:15, 11 October 2023

2023-10-11T06:15:32Z

← Older revision		Revision as of 06:15, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6dxt' size='340' side='right'caption='[[6dxt]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6dxt' size='340' side='right'caption='[[6dxt]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dxt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DXT FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dxt]] 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=6DXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DXT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHY:3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic+acid'>HHY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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]] 1.95Å</td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">USP5, ISOT ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHY:3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic+acid'>HHY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=6dxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxt OCA], [https://pdbe.org/6dxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dxt RCSB], [https://www.ebi.ac.uk/pdbsum/6dxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxt 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=6dxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxt OCA], [https://pdbe.org/6dxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dxt RCSB], [https://www.ebi.ac.uk/pdbsum/6dxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/UBP5_HUMAN UBP5_HUMAN]] Cleaves linear and branched multiubiquitin polymers with a marked preference for branched polymers. Involved in unanchored 'Lys-48'-linked polyubiquitin disassembly. Binds linear and 'Lys-63'-linked polyubiquitin with a lower affinity. Knock-down of USP5 causes the accumulation of p53/TP53 and an increase in p53/TP53 transcriptional activity because the unanchored polyubiquitin that accumulates is able to compete with ubiquitinated p53/TP53 but not with MDM2 for proteasomal recognition.<ref>PMID:19098288</ref>		[https://www.uniprot.org/uniprot/UBP5_HUMAN UBP5_HUMAN] Cleaves linear and branched multiubiquitin polymers with a marked preference for branched polymers. Involved in unanchored 'Lys-48'-linked polyubiquitin disassembly. Binds linear and 'Lys-63'-linked polyubiquitin with a lower affinity. Knock-down of USP5 causes the accumulation of p53/TP53 and an increase in p53/TP53 transcriptional activity because the unanchored polyubiquitin that accumulates is able to compete with ubiquitinated p53/TP53 but not with MDM2 for proteasomal recognition.<ref>PMID:19098288</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Ubiquitinyl hydrolase 1]]~~		[[Category: Arrowsmith CM]]
	[[Category: Arrowsmith~~, C M~~]]		[[Category: Bountra C]]
	[[Category: Bountra, C]]		[[Category: Edwards AM]]
	[[Category: Edwards~~, A M~~]]		[[Category: Ferreira de Freitas R]]
	[[Category: ~~Franzoni, I~~]]		[[Category: Franzoni I]]
	[[Category: ~~Freitas, R Ferreira de~~]]		[[Category: Harding RJ]]
	[[Category: Harding~~, R J~~]]		[[Category: Mann MK]]
	[[Category: Mann~~, M K~~]]		[[Category: Ravichandran M]]
	[[Category: Ravichandran, M]]		[[Category: Schapira M]]
	~~[[Category: Structural genomic~~]]
	[[Category: Schapira, M]]
	~~[[Category: Deubiquitinase]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Sgc]]~~
	~~[[Category: Ubiquitin]]~~
	~~[[Category: Usp5~~]]

OCA at 12:23, 9 June 2021

2021-06-09T12:23:21Z

← Older revision		Revision as of 12:23, 9 June 2021
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	<StructureSection load='6dxt' size='340' side='right'caption='[[6dxt]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6dxt' size='340' side='right'caption='[[6dxt]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dxt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6DXT FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dxt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DXT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHY:3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic+acid'>HHY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHY:3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic+acid'>HHY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">USP5, ISOT ([https://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~~://proteopedia.org/fgij/fg.htm?mol=6dxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxt OCA], [~~http~~://pdbe.org/6dxt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dxt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dxt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxt ProSAT]</span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=6dxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxt OCA], [https://pdbe.org/6dxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dxt RCSB], [https://www.ebi.ac.uk/pdbsum/6dxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/UBP5_HUMAN UBP5_HUMAN]] Cleaves linear and branched multiubiquitin polymers with a marked preference for branched polymers. Involved in unanchored 'Lys-48'-linked polyubiquitin disassembly. Binds linear and 'Lys-63'-linked polyubiquitin with a lower affinity. Knock-down of USP5 causes the accumulation of p53/TP53 and an increase in p53/TP53 transcriptional activity because the unanchored polyubiquitin that accumulates is able to compete with ubiquitinated p53/TP53 but not with MDM2 for proteasomal recognition.<ref>PMID:19098288</ref>		[[https://www.uniprot.org/uniprot/UBP5_HUMAN UBP5_HUMAN]] Cleaves linear and branched multiubiquitin polymers with a marked preference for branched polymers. Involved in unanchored 'Lys-48'-linked polyubiquitin disassembly. Binds linear and 'Lys-63'-linked polyubiquitin with a lower affinity. Knock-down of USP5 causes the accumulation of p53/TP53 and an increase in p53/TP53 transcriptional activity because the unanchored polyubiquitin that accumulates is able to compete with ubiquitinated p53/TP53 but not with MDM2 for proteasomal recognition.<ref>PMID:19098288</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			USP5 disassembles unanchored polyubiquitin chains to recycle free monoubiquitin, and is one of the 12 ubiquitin specific proteases featuring a zinc finger ubiquitin-binding domain (ZnF-UBD). This distinct structural module has been associated with substrate positioning or allosteric modulation of catalytic activity, but its cellular function remains unclear. We screened a chemical library focused on the ZnF-UBD of USP5, crystallized hits in complex with the protein, and generated a preliminary structure-activity relationship, which enables the development of more potent and selective compounds. This work serves as a framework for the discovery of a chemical probe to delineate the function of USP5 ZnF-UBD in proteasomal degradation and other ubiquitin signaling pathways in health and disease.

			Discovery of Small Molecule Antagonists of the USP5 Zinc Finger Ubiquitin-Binding Domain.,Mann MK, Franzoni I, de Freitas RF, Tempel W, Houliston S, Smith L, Vedadi M, Arrowsmith CH, Harding RJ, Schapira M J Med Chem. 2019 Nov 27;62(22):10144-10155. doi: 10.1021/acs.jmedchem.9b00988., Epub 2019 Nov 12. PMID:31663737<ref>PMID:31663737</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6dxt" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 17:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ubiquitinyl hydrolase 1]]		[[Category: Ubiquitinyl hydrolase 1]]

OCA at 09:08, 11 November 2020

2020-11-11T09:08:54Z

← Older revision		Revision as of 09:08, 11 November 2020
Line 1:		Line 1:

	==Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoate==		==Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoate==
	<StructureSection load='6dxt' size='340' side='right' caption='[[6dxt]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6dxt' size='340' side='right'caption='[[6dxt]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dxt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DXT FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dxt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6DXT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHY:3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic+acid'>HHY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHY:3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic+acid'>HHY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6dxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxt OCA], [http://pdbe.org/6dxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dxt RCSB], [http://www.ebi.ac.uk/pdbsum/6dxt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxt 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=6dxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxt OCA], [http://pdbe.org/6dxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dxt RCSB], [http://www.ebi.ac.uk/pdbsum/6dxt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/UBP5_HUMAN UBP5_HUMAN]] Cleaves linear and branched multiubiquitin polymers with a marked preference for branched polymers. Involved in unanchored 'Lys-48'-linked polyubiquitin disassembly. Binds linear and 'Lys-63'-linked polyubiquitin with a lower affinity. Knock-down of USP5 causes the accumulation of p53/TP53 and an increase in p53/TP53 transcriptional activity because the unanchored polyubiquitin that accumulates is able to compete with ubiquitinated p53/TP53 but not with MDM2 for proteasomal recognition.<ref>PMID:19098288</ref>		[[http://www.uniprot.org/uniprot/UBP5_HUMAN UBP5_HUMAN]] Cleaves linear and branched multiubiquitin polymers with a marked preference for branched polymers. Involved in unanchored 'Lys-48'-linked polyubiquitin disassembly. Binds linear and 'Lys-63'-linked polyubiquitin with a lower affinity. Knock-down of USP5 causes the accumulation of p53/TP53 and an increase in p53/TP53 transcriptional activity because the unanchored polyubiquitin that accumulates is able to compete with ubiquitinated p53/TP53 but not with MDM2 for proteasomal recognition.<ref>PMID:19098288</ref>

			==See Also==
			*[[Thioesterase 3D structures\|Thioesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Ubiquitinyl hydrolase 1]]		[[Category: Ubiquitinyl hydrolase 1]]
	[[Category: Arrowsmith, C M]]		[[Category: Arrowsmith, C M]]

OCA at 21:49, 9 August 2018

2018-08-09T21:49:52Z

← Older revision		Revision as of 21:49, 9 August 2018
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6dxt ~~is ON HOLD~~		==Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoate==
			<StructureSection load='6dxt' size='340' side='right' caption='[[6dxt]], [[Resolution\|resolution]] 1.95Å' scene=''>
	~~Authors~~: ~~Mann, M~~.K.~~, Harding, R~~.J., ~~Ravichandran~~, M., ~~Ferreira de Freitas~~, R., ~~Franzoni~~, I., ~~Bountra~~, C., ~~Edwards~~, A.M., ~~Arrowsmith, C~~.M., ~~Schapira, M~~.~~, Structural Genomics Consortium (SGC)~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[6dxt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DXT FirstGlance]. <br>
	~~Description~~: ~~Structure of USP5 zinc~~-~~finger ubiquitin binding domain co~~-~~crystallized with 3~~-(5-~~phenyl~~-1,3,~~4-oxadiazol-2-yl)propanoate~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HHY:3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic+acid'>HHY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <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=6dxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxt OCA], [http://pdbe.org/6dxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dxt RCSB], [http://www.ebi.ac.uk/pdbsum/6dxt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxt ProSAT]</span></td></tr>
			</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/UBP5_HUMAN UBP5_HUMAN]] Cleaves linear and branched multiubiquitin polymers with a marked preference for branched polymers. Involved in unanchored 'Lys-48'-linked polyubiquitin disassembly. Binds linear and 'Lys-63'-linked polyubiquitin with a lower affinity. Knock-down of USP5 causes the accumulation of p53/TP53 and an increase in p53/TP53 transcriptional activity because the unanchored polyubiquitin that accumulates is able to compete with ubiquitinated p53/TP53 but not with MDM2 for proteasomal recognition.<ref>PMID:19098288</ref>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Ubiquitinyl hydrolase 1]]
			[[Category: Arrowsmith, C M]]
			[[Category: Bountra, C]]
			[[Category: Edwards, A M]]
	[[Category: Franzoni, I]]		[[Category: Franzoni, I]]
			[[Category: Freitas, R Ferreira de]]
			[[Category: Harding, R J]]
			[[Category: Mann, M K]]
	[[Category: Ravichandran, M]]		[[Category: Ravichandran, M]]
	[[Category: ~~Arrowsmith, C.M~~]]		[[Category: Structural genomic]]
	[[Category: Schapira, M]]		[[Category: Schapira, M]]
	[[Category: ~~Ferreira De Freitas, R~~]]		[[Category: Deubiquitinase]]
	[[Category: ~~Bountra, C~~]]		[[Category: Hydrolase]]
	[[Category: ~~Mann, M.K~~]]		[[Category: Sgc]]
	[[Category: ~~Edwards, A.M]]~~		[[Category: Ubiquitin]]
	~~[[Category: Structural Genomics Consortium (Sgc)~~]]		[[Category: Usp5]]
	[[Category: ~~Harding, R.J~~]]

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

2018-07-11T04:06:10Z

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

← Older revision	Revision as of 04:06, 11 July 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6dxt is ON HOLD Authors: Mann, M.K., Harding, R.J., Ravichandran, M., Ferreira de Freitas, R., Franzoni, I., Bountra, C., Edwards, A.M., Arrowsmith,...

2018-07-11T04:06:08Z

New page: '''Unreleased structure''' The entry 6dxt is ON HOLD Authors: Mann, M.K., Harding, R.J., Ravichandran, M., Ferreira de Freitas, R., Franzoni, I., Bountra, C., Edwards, A.M., Arrowsmith,...

New page

'''Unreleased structure'''

The entry 6dxt is ON HOLD

Authors: Mann, M.K., Harding, R.J., Ravichandran, M., Ferreira de Freitas, R., Franzoni, I., Bountra, C., Edwards, A.M., Arrowsmith, C.M., Schapira, M., Structural Genomics Consortium (SGC)

Description: Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoate
[[Category: Unreleased Structures]]
[[Category: Franzoni, I]]
[[Category: Ravichandran, M]]
[[Category: Arrowsmith, C.M]]
[[Category: Schapira, M]]
[[Category: Ferreira De Freitas, R]]
[[Category: Bountra, C]]
[[Category: Mann, M.K]]
[[Category: Edwards, A.M]]
[[Category: Structural Genomics Consortium (Sgc)]]
[[Category: Harding, R.J]]