5ohn - Revision history

OCA at 08:46, 9 October 2024

2024-10-09T08:46:40Z

← Older revision		Revision as of 08:46, 9 October 2024
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	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/~~UBP30_HUMAN UBP30_HUMAN~~] ~~Deubiquitinating enzyme tethered~~ to ~~the mitochondrial outer membrane that acts~~ as a ~~key inhibitor~~ of ~~mitophagy by counteracting~~ the ~~action~~ of ~~parkin~~ (~~PRKN~~)~~: hydrolyzes ubiquitin~~ attached ~~by parkin on~~ target ~~proteins~~, ~~such as RHOT1/MIRO1 and TOMM20, thereby blocking parkin's ability to drive mitophagy (PubMed:18287522, PubMed:24896179, PubMed~~:~~25527291, PubMed:25621951). Preferentially cleaves '~~Lys-6'- and 'Lys-~~11'~~-linked ~~polyubiquitin chains~~, ~~2 types~~ of ~~linkage that participate~~ to ~~mitophagic~~ signaling ~~(PubMed:25621951)~~. ~~Does not cleave efficiently~~ polyubiquitin ~~phosphorylated at 'Ser~~-~~65' (PubMed:25527291~~)~~. Acts~~ as ~~negative regulator~~ of ~~mitochondrial fusion by mediating deubiquitination of MFN1~~ and ~~MFN2 (By similarity)~~.~~[UniProtKB:Q3UN04]<ref>PMID:18287522</ref> <ref>PMID:24896179</ref>~~ <ref>PMID:~~25527291~~</ref> <ref>PMID:~~25621951~~</ref>		[https://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 16:50, 13 December 2023

2023-12-13T16:50:36Z

← Older revision		Revision as of 16:50, 13 December 2023
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	==Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution)==		==Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution)==
	<StructureSection load='5ohn' size='340' side='right' caption='[[5ohn]], [[Resolution\|resolution]] 3.60Å' scene=''>		<StructureSection load='5ohn' size='340' side='right'caption='[[5ohn]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ohn]] is a 4 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=5OHN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OHN FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ohn]] is a 4 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=5OHN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OHN 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.6Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=AYE:PROP-2-EN-1-AMINE'>AYE</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AYE:PROP-2-EN-1-AMINE'>AYE</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">[[5ohk\|5ohk]]</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=5ohn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohn OCA], [https://pdbe.org/5ohn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ohn RCSB], [https://www.ebi.ac.uk/pdbsum/5ohn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohn ProSAT]</span></td></tr>
	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b></td><td class="sblockDat">USP30 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBB ([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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ohn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohn OCA], [~~http~~://pdbe.org/5ohn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ohn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ohn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/UBP30_HUMAN UBP30_HUMAN]] Deubiquitinating enzyme tethered to the mitochondrial outer membrane that acts as a key inhibitor of mitophagy by counteracting the action of parkin (PRKN): hydrolyzes ubiquitin attached by parkin on target proteins, such as RHOT1/MIRO1 and TOMM20, thereby blocking parkin's ability to drive mitophagy (PubMed:18287522, PubMed:24896179, PubMed:25527291, PubMed:25621951). Preferentially cleaves 'Lys-6'- and 'Lys-11'-linked polyubiquitin chains, 2 types of linkage that participate to mitophagic signaling (PubMed:25621951). Does not cleave efficiently polyubiquitin phosphorylated at 'Ser-65' (PubMed:25527291). Acts as negative regulator of mitochondrial fusion by mediating deubiquitination of MFN1 and MFN2 (By similarity).[UniProtKB:Q3UN04]<ref>PMID:18287522</ref> <ref>PMID:24896179</ref> <ref>PMID:25527291</ref> <ref>PMID:25621951</ref> [[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>		[https://www.uniprot.org/uniprot/UBP30_HUMAN UBP30_HUMAN] Deubiquitinating enzyme tethered to the mitochondrial outer membrane that acts as a key inhibitor of mitophagy by counteracting the action of parkin (PRKN): hydrolyzes ubiquitin attached by parkin on target proteins, such as RHOT1/MIRO1 and TOMM20, thereby blocking parkin's ability to drive mitophagy (PubMed:18287522, PubMed:24896179, PubMed:25527291, PubMed:25621951). Preferentially cleaves 'Lys-6'- and 'Lys-11'-linked polyubiquitin chains, 2 types of linkage that participate to mitophagic signaling (PubMed:25621951). Does not cleave efficiently polyubiquitin phosphorylated at 'Ser-65' (PubMed:25527291). Acts as negative regulator of mitochondrial fusion by mediating deubiquitination of MFN1 and MFN2 (By similarity).[UniProtKB:Q3UN04]<ref>PMID:18287522</ref> <ref>PMID:24896179</ref> <ref>PMID:25527291</ref> <ref>PMID:25621951</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5ohn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ohn" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Thioesterase 3D structures\|Thioesterase 3D structures]]
			*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: ~~Gersch, M~~]]		[[Category: Large Structures]]
	[[Category: ~~Komander, D~~]]		[[Category: Gersch M]]
	[[Category: ~~Deubiquitinase]]~~		[[Category: Komander D]]
	~~[[Category: Dub]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Ubiquitin]]~~
	~~[[Category: Usp~~]]

OCA at 10:13, 15 November 2017

2017-11-15T10:13:29Z

← Older revision		Revision as of 10:13, 15 November 2017
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	<StructureSection load='5ohn' size='340' side='right' caption='[[5ohn]], [[Resolution\|resolution]] 3.60Å' scene=''>		<StructureSection load='5ohn' size='340' side='right' caption='[[5ohn]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ohn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OHN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OHN FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ohn]] is a 4 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=5OHN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OHN 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AYE:PROP-2-EN-1-AMINE'>AYE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AYE:PROP-2-EN-1-AMINE'>AYE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ohk\|5ohk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ohk\|5ohk]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">USP30 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), UBB ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ohn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohn OCA], [http://pdbe.org/5ohn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ohn RCSB], [http://www.ebi.ac.uk/pdbsum/5ohn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohn 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=5ohn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ohn OCA], [http://pdbe.org/5ohn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ohn RCSB], [http://www.ebi.ac.uk/pdbsum/5ohn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ohn ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human]]
	[[Category: Gersch, M]]		[[Category: Gersch, M]]
	[[Category: Komander, D]]		[[Category: Komander, D]]

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

2017-10-04T09:14:53Z

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

← Older revision	Revision as of 09:14, 4 October 2017
(No difference)

OCA: New page: ==Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution)==