3b1l - Revision history

OCA at 14:03, 13 March 2024

2024-03-13T14:03:13Z

←Older revision		Revision as of 14:03, 13 March 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/PRKN_MOUSE PRKN_MOUSE] Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins (PubMed:32047033, PubMed:29311685). Substrates include SYT11 and VDAC1 (PubMed:32047033, PubMed:29311685). Other substrates are BCL2, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPTIN5, TOMM20, USP30, ZNF746, MIRO1 and AIMP2 (By similarity). Mediates monoubiquitination as well as 'Lys-6', 'Lys-11', 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context (PubMed:32047033, PubMed:25474007). Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation (By similarity). Mediates 'Lys-63'-linked polyubiquitination of a 22 kDa O-linked glycosylated isoform of SNCAIP, possibly playing a role in Lewy-body formation (By similarity). Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy (By similarity). Protects against mitochondrial dysfunction during cellular stress, by acting downstream of PINK1 to coordinate mitochondrial quality control mechanisms that remove and replace dysfunctional mitochondrial components (PubMed:32047033, PubMed:25474007, PubMed:22082830, PubMed:24898855). Depending on the severity of mitochondrial damage and/or dysfunction, activity ranges from preventing apoptosis and stimulating mitochondrial biogenesis to regulating mitochondrial dynamics and eliminating severely damaged mitochondria via mitophagy (PubMed:32047033, PubMed:22082830, PubMed:24898855). Activation and recruitment onto the outer membrane of damaged/dysfunctional mitochondria (OMM) requires PINK1-mediated phosphorylation of both PRKN and ubiquitin (PubMed:25474007). After mitochondrial damage, functions with PINK1 to mediate the decision between mitophagy or preventing apoptosis by inducing either the poly- or monoubiquitination of VDAC1, respectively; polyubiquitination of VDAC1 promotes mitophagy, while monoubiquitination of VDAC1 decreases mitochondrial calcium influx which ultimately inhibits apoptosis (PubMed:32047033). When cellular stress results in irreversible mitochondrial damage, promotes the autophagic degradation of dysfunctional depolarized mitochondria (mitophagy) by promoting the ubiquitination of mitochondrial proteins such as TOMM20, RHOT1/MIRO1, MFN1 and USP30 (PubMed:21753002). Preferentially assembles 'Lys-6'-, 'Lys-11'- and 'Lys-63'-linked polyubiquitin chains, leading to mitophagy (By similarity). The PINK1-PRKN pathway also promotes fission of damaged mitochondria by PINK1-mediated phosphorylation which promotes the PRKN-dependent degradation of mitochondrial proteins involved in fission such as MFN2 (PubMed:24192653). This prevents the refusion of unhealthy mitochondria with the mitochondrial network or initiates mitochondrial fragmentation facilitating their later engulfment by autophagosomes (By similarity). Regulates motility of damaged mitochondria via the ubiquitination and subsequent degradation of MIRO1 and MIRO2; in motor neurons, this likely inhibits mitochondrial intracellular anterograde transport along the axons which probably increases the chance of the mitochondria undergoing mitophagy in the soma (By similarity). Involved in mitochondrial biogenesis via the 'Lys-48'-linked polyubiquitination of transcriptional repressor ZNF746/PARIS which leads to its subsequent proteasomal degradation and allows activation of the transcription factor PPARGC1A (By similarity). Limits the production of reactive oxygen species (ROS) (By similarity). Regulates cyclin-E during neuronal apoptosis (By similarity). In collaboration with CHPF isoform 2, may enhance cell viability and protect cells from oxidative stress (PubMed:22082830). Independently of its ubiquitin ligase activity, protects from apoptosis by the transcriptional repression of p53/TP53 (PubMed:19801972). May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity (By similarity). May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. May represent a tumor suppressor gene (By similarity).[UniProtKB:O60260]<ref>PMID:19801972</ref> <ref>PMID:21753002</ref> <ref>PMID:22082830</ref> <ref>PMID:24192653</ref> <ref>PMID:24898855</ref> <ref>PMID:25474007</ref> <ref>PMID:29311685</ref> <ref>PMID:32047033</ref>		[https://www.uniprot.org/uniprot/PRKN_MOUSE PRKN_MOUSE] Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins (PubMed:32047033, PubMed:29311685). Substrates include SYT11 and VDAC1 (PubMed:32047033, PubMed:29311685). Other substrates are BCL2, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPTIN5, TOMM20, USP30, ZNF746, MIRO1 and AIMP2 (By similarity). Mediates monoubiquitination as well as 'Lys-6', 'Lys-11', 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context (PubMed:32047033, PubMed:25474007). Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation (By similarity). Mediates 'Lys-63'-linked polyubiquitination of a 22 kDa O-linked glycosylated isoform of SNCAIP, possibly playing a role in Lewy-body formation (By similarity). Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy (By similarity). Protects against mitochondrial dysfunction during cellular stress, by acting downstream of PINK1 to coordinate mitochondrial quality control mechanisms that remove and replace dysfunctional mitochondrial components (PubMed:32047033, PubMed:25474007, PubMed:22082830, PubMed:24898855). Depending on the severity of mitochondrial damage and/or dysfunction, activity ranges from preventing apoptosis and stimulating mitochondrial biogenesis to regulating mitochondrial dynamics and eliminating severely damaged mitochondria via mitophagy (PubMed:32047033, PubMed:22082830, PubMed:24898855). Activation and recruitment onto the outer membrane of damaged/dysfunctional mitochondria (OMM) requires PINK1-mediated phosphorylation of both PRKN and ubiquitin (PubMed:25474007). After mitochondrial damage, functions with PINK1 to mediate the decision between mitophagy or preventing apoptosis by inducing either the poly- or monoubiquitination of VDAC1, respectively; polyubiquitination of VDAC1 promotes mitophagy, while monoubiquitination of VDAC1 decreases mitochondrial calcium influx which ultimately inhibits apoptosis (PubMed:32047033). When cellular stress results in irreversible mitochondrial damage, promotes the autophagic degradation of dysfunctional depolarized mitochondria (mitophagy) by promoting the ubiquitination of mitochondrial proteins such as TOMM20, RHOT1/MIRO1, MFN1 and USP30 (PubMed:21753002). Preferentially assembles 'Lys-6'-, 'Lys-11'- and 'Lys-63'-linked polyubiquitin chains, leading to mitophagy (By similarity). The PINK1-PRKN pathway also promotes fission of damaged mitochondria by PINK1-mediated phosphorylation which promotes the PRKN-dependent degradation of mitochondrial proteins involved in fission such as MFN2 (PubMed:24192653). This prevents the refusion of unhealthy mitochondria with the mitochondrial network or initiates mitochondrial fragmentation facilitating their later engulfment by autophagosomes (By similarity). Regulates motility of damaged mitochondria via the ubiquitination and subsequent degradation of MIRO1 and MIRO2; in motor neurons, this likely inhibits mitochondrial intracellular anterograde transport along the axons which probably increases the chance of the mitochondria undergoing mitophagy in the soma (By similarity). Involved in mitochondrial biogenesis via the 'Lys-48'-linked polyubiquitination of transcriptional repressor ZNF746/PARIS which leads to its subsequent proteasomal degradation and allows activation of the transcription factor PPARGC1A (By similarity). Limits the production of reactive oxygen species (ROS) (By similarity). Regulates cyclin-E during neuronal apoptosis (By similarity). In collaboration with CHPF isoform 2, may enhance cell viability and protect cells from oxidative stress (PubMed:22082830). Independently of its ubiquitin ligase activity, protects from apoptosis by the transcriptional repression of p53/TP53 (PubMed:19801972). May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity (By similarity). May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. May represent a tumor suppressor gene (By similarity).[UniProtKB:O60260]<ref>PMID:19801972</ref> <ref>PMID:21753002</ref> <ref>PMID:22082830</ref> <ref>PMID:24192653</ref> <ref>PMID:24898855</ref> <ref>PMID:25474007</ref> <ref>PMID:29311685</ref> <ref>PMID:32047033</ref>
-
-	==See Also==
-	*[[Ubiquitin protein ligase 3D structures\|Ubiquitin protein ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:29, 8 November 2023

2023-11-08T17:29:11Z

←Older revision		Revision as of 17:29, 8 November 2023
Line 3:		Line 3:
	<StructureSection load='3b1l' size='340' side='right'caption='[[3b1l]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3b1l' size='340' side='right'caption='[[3b1l]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B1L FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>~~[[~~2zeq~~\|~~2zeq~~]]~~</div>~~</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]] 1.85Å</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=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [https://pdbe.org/3b1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [https://www.ebi.ac.uk/pdbsum/3b1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b1l 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=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [https://pdbe.org/3b1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [https://www.ebi.ac.uk/pdbsum/3b1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b1l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~PRKN2_MOUSE PRKN2_MOUSE]~~] Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, ~~such as BCL2,~~ SYT11, CCNE1, GPR37, STUB1, ~~a 22 kDa O-linked glycosylated isoform of~~ SNCAIP, ~~SEPT5~~, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. ~~Promotes~~ the autophagic degradation of dysfunctional depolarized mitochondria. ~~Mediates~~ 'Lys-48'-linked ~~polyubiquitination of ZNF746~~, ~~followed~~ by degradation of ~~ZNF746~~ by the ~~proteasome~~; ~~possibly playing a role~~ in ~~role~~ in ~~regulation~~ of ~~neuron death~~. Limits the production of reactive oxygen species (ROS). ~~Loss~~ of ~~this~~ ubiquitin ligase activity ~~appears to be~~ the ~~mechanism underlying pathogenesis~~ of ~~PARK2~~. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis~~. Regulates cyclin-E during neuronal apoptosis~~. May represent a tumor suppressor gene (By similarity).<ref>PMID:~~15105460~~</ref>	+	[https://www.uniprot.org/uniprot/PRKN_MOUSE PRKN_MOUSE] Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins (PubMed:32047033, PubMed:29311685). Substrates include SYT11 and VDAC1 (PubMed:32047033, PubMed:29311685). Other substrates are BCL2, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPTIN5, TOMM20, USP30, ZNF746, MIRO1 and AIMP2 (By similarity). Mediates monoubiquitination as well as 'Lys-6', 'Lys-11', 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context (PubMed:32047033, PubMed:25474007). Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation (By similarity). Mediates 'Lys-63'-linked polyubiquitination of a 22 kDa O-linked glycosylated isoform of SNCAIP, possibly playing a role in Lewy-body formation (By similarity). Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy (By similarity). Protects against mitochondrial dysfunction during cellular stress, by acting downstream of PINK1 to coordinate mitochondrial quality control mechanisms that remove and replace dysfunctional mitochondrial components (PubMed:32047033, PubMed:25474007, PubMed:22082830, PubMed:24898855). Depending on the severity of mitochondrial damage and/or dysfunction, activity ranges from preventing apoptosis and stimulating mitochondrial biogenesis to regulating mitochondrial dynamics and eliminating severely damaged mitochondria via mitophagy (PubMed:32047033, PubMed:22082830, PubMed:24898855). Activation and recruitment onto the outer membrane of damaged/dysfunctional mitochondria (OMM) requires PINK1-mediated phosphorylation of both PRKN and ubiquitin (PubMed:25474007). After mitochondrial damage, functions with PINK1 to mediate the decision between mitophagy or preventing apoptosis by inducing either the poly- or monoubiquitination of VDAC1, respectively; polyubiquitination of VDAC1 promotes mitophagy, while monoubiquitination of VDAC1 decreases mitochondrial calcium influx which ultimately inhibits apoptosis (PubMed:32047033). When cellular stress results in irreversible mitochondrial damage, promotes the autophagic degradation of dysfunctional depolarized mitochondria (mitophagy) by promoting the ubiquitination of mitochondrial proteins such as TOMM20, RHOT1/MIRO1, MFN1 and USP30 (PubMed:21753002). Preferentially assembles 'Lys-6'-, 'Lys-11'- and 'Lys-63'-linked polyubiquitin chains, leading to mitophagy (By similarity). The PINK1-PRKN pathway also promotes fission of damaged mitochondria by PINK1-mediated phosphorylation which promotes the PRKN-dependent degradation of mitochondrial proteins involved in fission such as MFN2 (PubMed:24192653). This prevents the refusion of unhealthy mitochondria with the mitochondrial network or initiates mitochondrial fragmentation facilitating their later engulfment by autophagosomes (By similarity). Regulates motility of damaged mitochondria via the ubiquitination and subsequent degradation of MIRO1 and MIRO2; in motor neurons, this likely inhibits mitochondrial intracellular anterograde transport along the axons which probably increases the chance of the mitochondria undergoing mitophagy in the soma (By similarity). Involved in mitochondrial biogenesis via the 'Lys-48'-linked polyubiquitination of transcriptional repressor ZNF746/PARIS which leads to its subsequent proteasomal degradation and allows activation of the transcription factor PPARGC1A (By similarity). Limits the production of reactive oxygen species (ROS) (By similarity). Regulates cyclin-E during neuronal apoptosis (By similarity). In collaboration with CHPF isoform 2, may enhance cell viability and protect cells from oxidative stress (PubMed:22082830). Independently of its ubiquitin ligase activity, protects from apoptosis by the transcriptional repression of p53/TP53 (PubMed:19801972). May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity (By similarity). May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. May represent a tumor suppressor gene (By similarity).[UniProtKB:O60260]<ref>PMID:19801972</ref> <ref>PMID:21753002</ref> <ref>PMID:22082830</ref> <ref>PMID:24192653</ref> <ref>PMID:24898855</ref> <ref>PMID:25474007</ref> <ref>PMID:29311685</ref> <ref>PMID:32047033</ref>

	==See Also==		==See Also==
Line 17:		Line 17:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Amami, Y]]	+	[[Category: Amami Y]]
-	[[Category: Ikemiya, A]]	+	[[Category: Ikemiya A]]
-	[[Category: In, Y]]	+	[[Category: In Y]]
-	[[Category: Ishida, T]]	+	[[Category: Ishida T]]
-	[[Category: Tomoo, K]]	+	[[Category: Tomoo K]]
-	~~[[Category: Alfa-beta-protein]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Parkin]]~~	+
-	~~[[Category: Proteasome]]~~	+
-	~~[[Category: Ubiquitin~~]]	+

OCA at 07:40, 2 February 2022

2022-02-02T07:40:08Z

←Older revision		Revision as of 07:40, 2 February 2022
Line 3:		Line 3:
	<StructureSection load='3b1l' size='340' side='right'caption='[[3b1l]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3b1l' size='340' side='right'caption='[[3b1l]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3B1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B1L FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zeq\|2zeq]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zeq\|2zeq]]</div></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=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [~~http~~://pdbe.org/3b1l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3b1l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3b1l 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=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [https://pdbe.org/3b1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [https://www.ebi.ac.uk/pdbsum/3b1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b1l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PRKN2_MOUSE PRKN2_MOUSE]] Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene (By similarity).<ref>PMID:15105460</ref>	+	[[https://www.uniprot.org/uniprot/PRKN2_MOUSE PRKN2_MOUSE]] Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene (By similarity).<ref>PMID:15105460</ref>

	==See Also==		==See Also==

OCA at 07:39, 29 April 2020

2020-04-29T07:39:35Z

←Older revision		Revision as of 07:39, 29 April 2020
Line 1:		Line 1:

	==Crystal Structure of parkin ubiquitin-like domain R33Q mutant==		==Crystal Structure of parkin ubiquitin-like domain R33Q mutant==
-	<StructureSection load='3b1l' size='340' side='right' caption='[[3b1l]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='3b1l' size='340' side='right'caption='[[3b1l]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3B1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3B1L FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zeq\|2zeq]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zeq\|2zeq]]</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=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [http://pdbe.org/3b1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [http://www.ebi.ac.uk/pdbsum/3b1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b1l 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=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [http://pdbe.org/3b1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [http://www.ebi.ac.uk/pdbsum/3b1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b1l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 11:		Line 11:

	==See Also==		==See Also==
-	*[[Ubiquitin protein ligase\|Ubiquitin protein ligase]]	+	*[[Ubiquitin protein ligase 3D structures\|Ubiquitin protein ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Amami, Y]]		[[Category: Amami, Y]]

OCA at 07:26, 25 July 2018

2018-07-25T07:26:04Z

←Older revision		Revision as of 07:26, 25 July 2018
Line 3:		Line 3:
	<StructureSection load='3b1l' size='340' side='right' caption='[[3b1l]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3b1l' size='340' side='right' caption='[[3b1l]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B1L FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zeq\|2zeq]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zeq\|2zeq]]</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=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [http://pdbe.org/3b1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [http://www.ebi.ac.uk/pdbsum/3b1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b1l 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=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [http://pdbe.org/3b1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [http://www.ebi.ac.uk/pdbsum/3b1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b1l ProSAT]</span></td></tr>
Line 16:		Line 16:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mus musculus~~]]	+	[[Category: Lk3 transgenic mice]]
	[[Category: Amami, Y]]		[[Category: Amami, Y]]
	[[Category: Ikemiya, A]]		[[Category: Ikemiya, A]]

OCA at 15:56, 4 August 2016

2016-08-04T15:56:46Z

←Older revision		Revision as of 15:56, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of parkin ubiquitin-like domain R33Q mutant==		==Crystal Structure of parkin ubiquitin-like domain R33Q mutant==
	<StructureSection load='3b1l' size='340' side='right' caption='[[3b1l]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3b1l' size='340' side='right' caption='[[3b1l]], [[Resolution\|resolution]] 1.85Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B1L FirstGlance]. <br>		<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B1L FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zeq\|2zeq]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zeq\|2zeq]]</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=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [http://www.ebi.ac.uk/pdbsum/3b1l PDBsum]</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=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [http://pdbe.org/3b1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [http://www.ebi.ac.uk/pdbsum/3b1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b1l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 10:47, 25 December 2014

2014-12-25T10:47:19Z

←Older revision		Revision as of 10:47, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B1L FirstGlance]. <br>		<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B1L FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zeq\|2zeq]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zeq\|2zeq]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [http://www.ebi.ac.uk/pdbsum/3b1l PDBsum]</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=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [http://www.ebi.ac.uk/pdbsum/3b1l PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PRKN2_MOUSE PRKN2_MOUSE]] Functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, STUB1, a 22 kDa O-linked glycosylated isoform of SNCAIP, SEPT5, ZNF746 and AIMP2. Mediates monoubiquitination as well as 'Lys-48'-linked and 'Lys-63'-linked polyubiquitination of substrates depending on the context. Participates in the removal and/or detoxification of abnormally folded or damaged protein by mediating 'Lys-63'-linked polyubiquitination of misfolded proteins such as PARK7: 'Lys-63'-linked polyubiquitinated misfolded proteins are then recognized by HDAC6, leading to their recruitment to aggresomes, followed by degradation. Mediates 'Lys-63'-linked polyubiquitination of SNCAIP, possibly playing a role in Lewy-body formation. Mediates monoubiquitination of BCL2, thereby acting as a positive regulator of autophagy. Promotes the autophagic degradation of dysfunctional depolarized mitochondria. Mediates 'Lys-48'-linked polyubiquitination of ZNF746, followed by degradation of ZNF746 by the proteasome; possibly playing a role in role in regulation of neuron death. Limits the production of reactive oxygen species (ROS). Loss of this ubiquitin ligase activity appears to be the mechanism underlying pathogenesis of PARK2. May protect neurons against alpha synuclein toxicity, proteasomal dysfunction, GPR37 accumulation, and kainate-induced excitotoxicity. May play a role in controlling neurotransmitter trafficking at the presynaptic terminal and in calcium-dependent exocytosis. Regulates cyclin-E during neuronal apoptosis. May represent a tumor suppressor gene (By similarity).<ref>PMID:15105460</ref>
		+
		+	==See Also==
		+	*[[Ubiquitin protein ligase\|Ubiquitin protein ligase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Amami, Y.]]	+	[[Category: Amami, Y]]
-	[[Category: Ikemiya, A.]]	+	[[Category: Ikemiya, A]]
-	[[Category: In, Y.]]	+	[[Category: In, Y]]
-	[[Category: Ishida, T.]]	+	[[Category: Ishida, T]]
-	[[Category: Tomoo, K.]]	+	[[Category: Tomoo, K]]
	[[Category: Alfa-beta-protein]]		[[Category: Alfa-beta-protein]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 11:04, 14 May 2014

2014-05-14T11:04:13Z

←Older revision		Revision as of 11:04, 14 May 2014
Line 1:		Line 1:
-	~~[[Image:3b1l.jpg\|left\|200px]]~~	+	==Crystal Structure of parkin ubiquitin-like domain R33Q mutant==
-		+	<StructureSection load='3b1l' size='340' side='right' caption='[[3b1l]], [[Resolution\|resolution]] 1.85Å' scene=''>
-	~~{{STRUCTURE_3b1l\| PDB=3b1l \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3b1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B1L FirstGlance]. <br>
-	===Crystal Structure of parkin ubiquitin-like domain R33Q mutant===	+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zeq\|2zeq]]</td></tr>
-		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3b1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b1l RCSB], [http://www.ebi.ac.uk/pdbsum/3b1l PDBsum]</span></td></tr>
-		+	<table>
-	==~~About this Structure~~==	+	__TOC__
-	[[3b1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA].	+	</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Amami, Y.]]		[[Category: Amami, Y.]]

OCA at 07:41, 4 July 2012

2012-07-04T07:41:58Z

←Older revision		Revision as of 07:41, 4 July 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3b1l.jpg\|left\|200px]]

-	~~The entry~~ 3b1l ~~is ON HOLD~~ ~~until Jul 04 2013~~	+	{{STRUCTURE_3b1l\| PDB=3b1l \| SCENE= }}

-	~~Authors: Tomoo, K., Ikemiya, A., Amami, Y., In, Y., Ishida, T.~~	+	===Crystal Structure of parkin ubiquitin-like domain R33Q mutant===

-	~~Description: Crystal~~ Structure ~~of parkin ubiquitin~~-~~like domain R33Q mutant~~	+
		+	==About this Structure==
		+	[[3b1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1L OCA].
		+	[[Category: Mus musculus]]
		+	[[Category: Amami, Y.]]
		+	[[Category: Ikemiya, A.]]
		+	[[Category: In, Y.]]
		+	[[Category: Ishida, T.]]
		+	[[Category: Tomoo, K.]]
		+	[[Category: Alfa-beta-protein]]
		+	[[Category: Ligase]]
		+	[[Category: Parkin]]
		+	[[Category: Proteasome]]
		+	[[Category: Ubiquitin]]

OCA at 08:30, 30 October 2011

2011-10-30T08:30:28Z

←Older revision		Revision as of 08:30, 30 October 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3b1l is ON HOLD	+	The entry 3b1l is ON HOLD until Jul 04 2013

	Authors: Tomoo, K., Ikemiya, A., Amami, Y., In, Y., Ishida, T.		Authors: Tomoo, K., Ikemiya, A., Amami, Y., In, Y., Ishida, T.

	Description: Crystal Structure of parkin ubiquitin-like domain R33Q mutant		Description: Crystal Structure of parkin ubiquitin-like domain R33Q mutant