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| - | ==Ser65 phosphorylated ubiquitin, major conformation== | + | ==Crystal Structure of Parkin== |
| - | <StructureSection load='4wzp' size='340' side='right' caption='[[4wzp]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='Cc4k95-1.pdb' size='340' side='right' caption='[[4k95]], [[Resolution|resolution]] 6.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4wzp]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WZP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4k95]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K95 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K95 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=SEP:PHOSPHOSERINE'>SEP</scene></td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4k7d|4k7d]]</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ubq|1ubq]]</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Park2, Prkn ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</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=4wzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wzp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wzp RCSB], [http://www.ebi.ac.uk/pdbsum/4wzp 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=4k95 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k95 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k95 RCSB], [http://www.ebi.ac.uk/pdbsum/4k95 PDBsum]</span></td></tr> |
| | </table> | | </table> |
| | + | ==Structure== |
| | + | Parkin is composed of six different domains: IBR, RING1, RING2, RING0, REP, and UBI. Four of these domains contain zinc fingers that are common characteristics of the RBR family. The zinc finger found in UBI is unique to parkin. IBR contains one of these zinc fingers along with a hinge that connects to RING1, which allows for flexibility and function. RING1 contains an E2 binding site and is the only domain in parkin to contain a C3HC4 cross-brace zinc coordination topology, which is found in other RING fingers. RING2 is very similar to IBR but RING2 contains a catalytic site that coordinates two zinc atoms. RING2 also mediates the hydrophobic groove found in RING0. RING0 is composed of four subdomains that have interdomain interactions. RING0 is a zinc-binding fold that connects RING1 and RING2. It has extensive hydrophobic interactions with RING2. RING0 also has two zinc atoms that are coordinated by four zinc-binding loops. REP is composed of an alpha helix surrounded by unstructured regions that hold it together. It primarily serves as a linker between IBR and RING2. UBI is an ubiquitin-like domain with a 60 amino acid linker. The zinc finger found in UBI is unique to parkin. |
| | == Function == | | == Function == |
| - | [[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> | + | [[http://www.uniprot.org/uniprot/PRKN2_RAT PRKN2_RAT]] 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). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| - | The protein kinase PINK1 was recently shown to phosphorylate ubiquitin (Ub) on Ser65, and phosphoUb activates the E3 ligase Parkin allosterically. Here, we show that PINK1 can phosphorylate every Ub in Ub chains. Moreover, Ser65 phosphorylation alters Ub structure, generating two conformations in solution. A crystal structure of the major conformation resembles Ub but has altered surface properties. NMR reveals a second phosphoUb conformation in which beta5-strand slippage retracts the C-terminal tail by two residues into the Ub core. We further show that phosphoUb has no effect on E1-mediated E2 charging but can affect discharging of E2 enzymes to form polyUb chains. Notably, UBE2R1- (CDC34), UBE2N/UBE2V1- (UBC13/UEV1A), TRAF6- and HOIP-mediated chain assembly is inhibited by phosphoUb. While Lys63-linked poly-phosphoUb is recognized by the TAB2 NZF Ub binding domain (UBD), 10 out of 12 deubiquitinases (DUBs), including USP8, USP15 and USP30, are impaired in hydrolyzing phosphoUb chains. Hence, Ub phosphorylation has repercussions for ubiquitination and deubiquitination cascades beyond Parkin activation and may provide an independent layer of regulation in the Ub system. | + | Mutations in the Parkin gene are responsible for an autosomal recessive form of Parkinson's disease. The parkin protein is a RING-In-Between-RING (RBR) E3 ubiquitin ligase, which exhibits low basal activity. Here, we describe the crystal structure of full-length parkin. The structure shows parkin in an auto-inhibited state and provides insight into how it is activated. RING0 occludes the ubiquitin acceptor site Cys431 in RING2, whereas a repressor element of parkin (REP) binds RING1 and blocks its E2-binding site. Mutations that disrupted these inhibitory interactions activated parkin both in vitro and in cells. Parkin is neuroprotective and these findings may provide a structural and mechanistic framework for enhancing parkin activity. |
| | | | |
| - | Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis.,Wauer T, Swatek KN, Wagstaff JL, Gladkova C, Pruneda JN, Michel MA, Gersch M, Johnson CM, Freund SM, Komander D EMBO J. 2014 Dec 19. pii: e201489847. PMID:25527291<ref>PMID:25527291</ref> | + | Structure of Parkin Reveals Mechanisms for Ubiquitin Ligase Activation.,Trempe JF, Sauve V, Grenier K, Seirafi M, Tang MY, Menade M, Al-Abdul-Wahid S, Krett J, Wong K, Kozlov G, Nagar B, Fon EA, Gehring K Science. 2013 May 9. PMID:23661642<ref>PMID:23661642</ref> |
| | | | |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ubiquitin protein ligase|Ubiquitin protein ligase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Freund, S M.V]] | + | [[Category: Rattus norvegicus]] |
| - | [[Category: Komander, D]] | + | [[Category: Gehring, K]] |
| - | [[Category: Wagstaff, J]] | + | [[Category: Kozlov, G]] |
| - | [[Category: Wauer, T]] | + | [[Category: Menade, M]] |
| - | [[Category: Mitophagy]] | + | [[Category: Nagar, B]] |
| - | [[Category: Parkin]] | + | [[Category: Sauve, V]] |
| - | [[Category: Phosphorylation]] | + | [[Category: Seirafi, M]] |
| - | [[Category: Pink1]] | + | [[Category: Trempe, J F]] |
| - | [[Category: Posttranslational modification]] | + | [[Category: Ligase]] |
| - | [[Category: Signaling protein]] | + | [[Category: Mitochondria]] |
| | + | [[Category: Rbr ubiquitin ligase]] |
| | + | [[Category: Ring domain]] |
| | + | [[Category: Ubch7]] |
| | + | [[Category: Ubiquitin]] |
| | + | [[Category: Ubiquitin-like domain]] |
| | + | [[Category: Zinc finger]] |
| Structural highlights
Structure
Parkin is composed of six different domains: IBR, RING1, RING2, RING0, REP, and UBI. Four of these domains contain zinc fingers that are common characteristics of the RBR family. The zinc finger found in UBI is unique to parkin. IBR contains one of these zinc fingers along with a hinge that connects to RING1, which allows for flexibility and function. RING1 contains an E2 binding site and is the only domain in parkin to contain a C3HC4 cross-brace zinc coordination topology, which is found in other RING fingers. RING2 is very similar to IBR but RING2 contains a catalytic site that coordinates two zinc atoms. RING2 also mediates the hydrophobic groove found in RING0. RING0 is composed of four subdomains that have interdomain interactions. RING0 is a zinc-binding fold that connects RING1 and RING2. It has extensive hydrophobic interactions with RING2. RING0 also has two zinc atoms that are coordinated by four zinc-binding loops. REP is composed of an alpha helix surrounded by unstructured regions that hold it together. It primarily serves as a linker between IBR and RING2. UBI is an ubiquitin-like domain with a 60 amino acid linker. The zinc finger found in UBI is unique to parkin.
Function
[PRKN2_RAT] 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).
Publication Abstract from PubMed
Mutations in the Parkin gene are responsible for an autosomal recessive form of Parkinson's disease. The parkin protein is a RING-In-Between-RING (RBR) E3 ubiquitin ligase, which exhibits low basal activity. Here, we describe the crystal structure of full-length parkin. The structure shows parkin in an auto-inhibited state and provides insight into how it is activated. RING0 occludes the ubiquitin acceptor site Cys431 in RING2, whereas a repressor element of parkin (REP) binds RING1 and blocks its E2-binding site. Mutations that disrupted these inhibitory interactions activated parkin both in vitro and in cells. Parkin is neuroprotective and these findings may provide a structural and mechanistic framework for enhancing parkin activity.
Structure of Parkin Reveals Mechanisms for Ubiquitin Ligase Activation.,Trempe JF, Sauve V, Grenier K, Seirafi M, Tang MY, Menade M, Al-Abdul-Wahid S, Krett J, Wong K, Kozlov G, Nagar B, Fon EA, Gehring K Science. 2013 May 9. PMID:23661642[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Trempe JF, Sauve V, Grenier K, Seirafi M, Tang MY, Menade M, Al-Abdul-Wahid S, Krett J, Wong K, Kozlov G, Nagar B, Fon EA, Gehring K. Structure of Parkin Reveals Mechanisms for Ubiquitin Ligase Activation. Science. 2013 May 9. PMID:23661642 doi:10.1126/science.1237908
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