5oat - Revision history

OCA at 09:38, 6 December 2023

OCA — Wed, 06 Dec 2023 09:38:38 GMT

←Older revision		Revision as of 09:38, 6 December 2023
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	<StructureSection load='5oat' size='340' side='right'caption='[[5oat]], [[Resolution\|resolution]] 2.78Å' scene=''>		<StructureSection load='5oat' size='340' side='right'caption='[[5oat]], [[Resolution\|resolution]] 2.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oat]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OAT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oat]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Tribolium_castaneum Tribolium castaneum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OAT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.78Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></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=5oat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oat OCA], [~~http~~://pdbe.org/5oat PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5oat RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5oat PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5oat 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=5oat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oat OCA], [https://pdbe.org/5oat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oat RCSB], [https://www.ebi.ac.uk/pdbsum/5oat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oat ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PINK1_TRICA PINK1_TRICA] Acts as a serine/threonine-protein kinase (PubMed:25474007, PubMed:26784449, PubMed:29475881, PubMed:32484300, PubMed:28980524, PubMed:24751536, PubMed:26116755, PubMed:29991771). Exhibits a substrate preference for proline at position P+1 and a general preference at several residues for basic residues such as arginine (PubMed:22645651). Also exhibits moderate preferences for a phosphotyrosine at position P-3 and a tryptophan at P-5 (PubMed:22645651). Critical to mitochondrial homeostasis it mediates several pathways that maintain mitochondrial health and function (By similarity). Protects against mitochondrial dysfunction during cellular stress by phosphorylating mitochondrial proteins such as park and likely Drp1, to coordinate mitochondrial quality control mechanisms that remove and replace dysfunctional mitochondrial components (PubMed:25474007, PubMed:32484300, PubMed:28980524, PubMed:24751536, PubMed:26116755, PubMed:29991771). 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 (By similarity). Appears to be particularly important in maintaining the physiology and function of cells with high energy demands that are undergoing stress or altered metabolic environment, including spermatids, muscle cells and neurons such as the dopaminergic (DA) neurons (By similarity). Mediates the translocation and activation of park at the outer membrane (OMM) of dysfunctional/depolarized mitochondria (PubMed:25474007, PubMed:26116755). At the OMM of damaged mitochondria, phosphorylates pre-existing polyubiquitin chains, the Pink1-phosphorylated polyubiquitin then recruits park from the cytosol to the OMM where park is fully activated by phosphorylation at 'Ser-80' by Pink1 (PubMed:24751536, PubMed:25474007, PubMed:29475881, PubMed:26116755, PubMed:29991771). When cellular stress results in irreversible mitochondrial damage, functions with park to promote the clearance of dysfunctional and/or depolarized mitochondria by selective autophagy (mitophagy) (By similarity). The Pink1-park pathway also promotes fission and/or inhibits fusion of damaged mitochondria, by phosphorylating and thus promoting the park-dependent degradation of proteins involved in mitochondrial fusion/fission such as Marf, Opa1 and fzo (By similarity). This prevents the refusion of unhealthy mitochondria with the mitochondrial network or initiates mitochondrial fragmentation facilitating their later engulfment by autophagosomes (By similarity). Also likely to promote mitochondrial fission independently of park and Atg7-mediated mitophagy, via the phosphorylation and activation of Drp1 (PubMed:32484300). Regulates motility of damaged mitochondria by phosphorylating Miro which likely promotes its park-dependent degradation by the proteasome; in motor neurons, this inhibits mitochondrial intracellular anterograde transport along the axons which probably increases the chance of the mitochondria being eliminated in the soma (By similarity). The Pink1-park pathway is also involved in mitochondrial regeneration processes such as promoting mitochondrial biogenesis, activating localized mitochondrial repair, promoting selective turnover of mitochondrial proteins and initiating the mitochondrial import of endogenous proteins (By similarity). Involved in mitochondrial biogenesis by promoting the park-dependent ubiquitination of transcriptional repressor Paris which leads to its subsequent proteasomal degradation and allows activation of the transcription factor srl (By similarity). Functions with park to promote localized mitochondrial repair by activating the translation of specific nuclear-encoded mitochondrial RNAs (nc-mtRNAs) on the mitochondrial surface, including several key electron transport chain component nc-mtRNAs (By similarity). During oogenesis, phosphorylates and inactivates larp on the membrane of defective mitochondria, thus impairing local translation and mtDNA replication and consequently, reducing transmission of deleterious mtDNA mutations to the mature oocyte (By similarity). Phosphorylates the mitochondrial acyl-CoA dehydrogenase Mcad, and appears to be important for maintaining fatty acid and amino acid metabolism via a mechanism that is independent of it's role in maintaining production of ATP (By similarity). Exhibits a substrate preference for proline at position P+1 and a general preference at several residues for basic residues such as arginine (PubMed:22645651). Also exhibits moderate preferences for a phosphotyrosine at position P-3 and a tryptophan at P-5 (PubMed:22645651).[UniProtKB:Q0KHV6]<ref>PMID:22645651</ref> <ref>PMID:24751536</ref> <ref>PMID:25474007</ref> <ref>PMID:26116755</ref> <ref>PMID:26784449</ref> <ref>PMID:28980524</ref> <ref>PMID:29475881</ref> <ref>PMID:29991771</ref> <ref>PMID:32484300</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Aalten, D M.F van~~]]	+	[[Category: Tribolium castaneum]]
-	[[Category: Kumar, A]]	+	[[Category: Kumar A]]
-	[[Category: Muqit~~, M M.K~~]]	+	[[Category: Muqit MMK]]
-	[[Category: Peggie, M]]	+	[[Category: Peggie M]]
-	[[Category: Raimi~~, O G~~]]	+	[[Category: Raimi OG]]
-	[[Category: Tamjar, J]]	+	[[Category: Tamjar J]]
-	[[Category: Waddell~~, A Y~~]]	+	[[Category: Waddell AY]]
-	[[Category: Woodroof~~, H I~~]]	+	[[Category: Woodroof HI]]
-	[[Category: ~~Kinase]]~~	+	[[Category: Van Aalten DMF]]
-	~~[[Category: Kinase for phosphorylation~~]]	+

OCA at 12:20, 26 August 2020

OCA — Wed, 26 Aug 2020 12:20:01 GMT

←Older revision		Revision as of 12:20, 26 August 2020
Line 1:		Line 1:

	==PINK1 structure==		==PINK1 structure==
-	<StructureSection load='5oat' size='340' side='right' caption='[[5oat]], [[Resolution\|resolution]] 2.78Å' scene=''>	+	<StructureSection load='5oat' size='340' side='right'caption='[[5oat]], [[Resolution\|resolution]] 2.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oat]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OAT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oat]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OAT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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='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='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=5oat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oat OCA], [http://pdbe.org/5oat PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oat RCSB], [http://www.ebi.ac.uk/pdbsum/5oat PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oat 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=5oat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oat OCA], [http://pdbe.org/5oat PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oat RCSB], [http://www.ebi.ac.uk/pdbsum/5oat PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oat ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5oat" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5oat" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Serine/threonine protein kinase 3D structures\|Serine/threonine protein kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Aalten, D M.F van]]		[[Category: Aalten, D M.F van]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]

OCA at 06:52, 18 October 2017

OCA — Wed, 18 Oct 2017 06:52:05 GMT

←Older revision		Revision as of 06:52, 18 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5oat is ~~ON HOLD until Paper~~ Publication	+	==PINK1 structure==
		+	<StructureSection load='5oat' size='340' side='right' caption='[[5oat]], [[Resolution\|resolution]] 2.78Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5oat]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OAT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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='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=5oat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oat OCA], [http://pdbe.org/5oat PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oat RCSB], [http://www.ebi.ac.uk/pdbsum/5oat PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oat ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mutations in the human kinase PINK1 (hPINK1) are associated with autosomal recessive early-onset Parkinson's disease (PD). hPINK1 activates Parkin E3 ligase activity, involving phosphorylation of ubiquitin and the Parkin ubiquitin-like (Ubl) domain via as yet poorly understood mechanisms. hPINK1 is unusual amongst kinases due to the presence of three loop insertions of unknown function. We report the structure of Tribolium castaneum PINK1 (TcPINK1), revealing several unique extensions to the canonical protein kinase fold. The third insertion, together with autophosphorylation at residue Ser205, contributes to formation of a bowl-shaped binding site for ubiquitin. We also define a novel structural element within the second insertion that is held together by a distal loop that is critical for TcPINK1 activity. The structure of TcPINK1 explains how PD-linked mutations that lie within the kinase domain result in hPINK1 loss-of-function and provides a platform for the exploration of small molecule modulators of hPINK1.

-	~~Authors~~:	+	Structure of PINK1 and mechanisms of Parkinson's disease associated mutations.,Kumar A, Tamjar J, Waddell AD, Woodroof HI, Raimi OG, Shaw AM, Peggie M, Muqit MM, van Aalten DM Elife. 2017 Oct 5;6. pii: e29985. doi: 10.7554/eLife.29985. PMID:28980524<ref>PMID:28980524</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5oat" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aalten, D M.F van]]
		+	[[Category: Kumar, A]]
		+	[[Category: Muqit, M M.K]]
		+	[[Category: Peggie, M]]
		+	[[Category: Raimi, O G]]
		+	[[Category: Tamjar, J]]
		+	[[Category: Waddell, A Y]]
		+	[[Category: Woodroof, H I]]
		+	[[Category: Kinase]]
		+	[[Category: Kinase for phosphorylation]]

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

OCA — Wed, 27 Sep 2017 12:13:30 GMT

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

←Older revision

Revision as of 12:13, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5oat is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 12:13:29 GMT

New page: '''Unreleased structure''' The entry 5oat is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5oat is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]