8ie8 - Revision history

OCA at 15:27, 4 October 2023

OCA — Wed, 04 Oct 2023 15:27:17 GMT

←Older revision		Revision as of 15:27, 4 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8ie8]] is a 1 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=8IE8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IE8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[8ie8]] is a 1 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=8IE8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IE8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P5O:5-[(~{E})-2-(3-methoxy-4-oxidanyl-phenyl)ethenyl]benzene-1,3-diol'>P5O</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.75Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P5O:5-[(~{E})-2-(3-methoxy-4-oxidanyl-phenyl)ethenyl]benzene-1,3-diol'>P5O</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=8ie8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ie8 OCA], [https://pdbe.org/8ie8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ie8 RCSB], [https://www.ebi.ac.uk/pdbsum/8ie8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ie8 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=8ie8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ie8 OCA], [https://pdbe.org/8ie8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ie8 RCSB], [https://www.ebi.ac.uk/pdbsum/8ie8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ie8 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 04:07, 25 May 2023

OCA — Thu, 25 May 2023 04:07:54 GMT

←Older revision		Revision as of 04:07, 25 May 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8ie8 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of DAPK1 in complex with isorhapontigenin==
		+	<StructureSection load='8ie8' size='340' side='right'caption='[[8ie8]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8ie8]] is a 1 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=8IE8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IE8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P5O:5-[(~{E})-2-(3-methoxy-4-oxidanyl-phenyl)ethenyl]benzene-1,3-diol'>P5O</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=8ie8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ie8 OCA], [https://pdbe.org/8ie8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ie8 RCSB], [https://www.ebi.ac.uk/pdbsum/8ie8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ie8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DAPK1_HUMAN DAPK1_HUMAN] Calcium/calmodulin-dependent serine/threonine kinase involved in multiple cellular signaling pathways that trigger cell survival, apoptosis, and autophagy. Regulates both type I apoptotic and type II autophagic cell deaths signal, depending on the cellular setting. The former is caspase-dependent, while the latter is caspase-independent and is characterized by the accumulation of autophagic vesicles. Phosphorylates PIN1 resulting in inhibition of its catalytic activity, nuclear localization, and cellular function. Phosphorylates TPM1, enhancing stress fiber formation in endothelial cells. Phosphorylates STX1A and significantly decreases its binding to STXBP1. Phosphorylates PRKD1 and regulates JNK signaling by binding and activating PRKD1 under oxidative stress. Phosphorylates BECN1, reducing its interaction with BCL2 and BCL2L1 and promoting the induction of autophagy. Phosphorylates TSC2, disrupting the TSC1-TSC2 complex and stimulating mTORC1 activity in a growth factor-dependent pathway. Phosphorylates RPS6, MYL9 and DAPK3. Acts as a signaling amplifier of NMDA receptors at extrasynaptic sites for mediating brain damage in stroke. Cerebral ischemia recruits DAPK1 into the NMDA receptor complex and it phosphorylates GRINB at Ser-1303 inducing injurious Ca(2+) influx through NMDA receptor channels, resulting in an irreversible neuronal death. Required together with DAPK3 for phosphorylation of RPL13A upon interferon-gamma activation which is causing RPL13A involvement in transcript-selective translation inhibition.<ref>PMID:7828849</ref> <ref>PMID:10629061</ref> <ref>PMID:11579085</ref> <ref>PMID:11980920</ref> <ref>PMID:12730201</ref> <ref>PMID:15367680</ref> <ref>PMID:17703233</ref> <ref>PMID:17895359</ref> <ref>PMID:18422656</ref> <ref>PMID:18195017</ref> <ref>PMID:18995835</ref> <ref>PMID:19180116</ref> <ref>PMID:18974095</ref> <ref>PMID:21497122</ref> <ref>PMID:21408167</ref> Isoform 2 cannot induce apoptosis but can induce membrane blebbing.<ref>PMID:7828849</ref> <ref>PMID:10629061</ref> <ref>PMID:11579085</ref> <ref>PMID:11980920</ref> <ref>PMID:12730201</ref> <ref>PMID:15367680</ref> <ref>PMID:17703233</ref> <ref>PMID:17895359</ref> <ref>PMID:18422656</ref> <ref>PMID:18195017</ref> <ref>PMID:18995835</ref> <ref>PMID:19180116</ref> <ref>PMID:18974095</ref> <ref>PMID:21497122</ref> <ref>PMID:21408167</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Death-associated protein kinase 1 (DAPK1), a Ca2+/calmodulin-regulated serine/threonine kinase, regulates cell apoptosis and autophagy and has been implicated in the pathogenesis of Alzheimer's disease (AD). Targeting DAPK1 may be a promising approach for treating AD. In our previous study, we found that a natural polyphenol, resveratrol (1), is a moderate DAPK1 inhibitor. In the present study, we investigated the interactions between natural and synthetic derivatives of 1 and DAPK1. Binding assays including intrinsic fluorescence quenching, protein thermal shift and isothermal titration calorimetry indicated that oxyresveratrol (3), a hydroxylated derivative, and pinostilbene (5), a methoxylated derivative, bind to DAPK1 with comparable affinity to 1. The enzymatic assay showed that 3 more effectively inhibits the intrinsic ATPase activity of DAPK1 compared with 1. Crystallographic analysis revealed that the binding modes of the methoxylated derivatives were different from those of 1 and 3, resulting in a unique interaction. Our results suggest that 3 may be helpful in treating AD and provide a clue for the development of promising DAPK1 inhibitors.

-	~~Authors: Yokoyama~~, T.	+	Characterization of the molecular interactions between resveratrol derivatives and death-associated protein kinase 1.,Yokoyama T, Kusaka K FEBS J. 2023 May 12. doi: 10.1111/febs.16817. PMID:37171222<ref>PMID:37171222</ref>

-	~~Description: Crystal structure~~ of ~~DAPK1 in complex with isorhapontigenin~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Yokoyama, T]]	+	<div class="pdbe-citations 8ie8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Yokoyama T]]

OCA at 05:00, 7 April 2023

OCA — Fri, 07 Apr 2023 05:00:55 GMT

←Older revision		Revision as of 05:00, 7 April 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8ie8 is ON HOLD	+	The entry 8ie8 is ON HOLD until Paper Publication

	Authors: Yokoyama, T.		Authors: Yokoyama, T.

OCA: Protected "8ie8" [edit=sysop:move=sysop]

OCA — Wed, 22 Feb 2023 10:40:33 GMT

Protected "8ie8" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:40, 22 February 2023

OCA: New page: '''Unreleased structure''' The entry 8ie8 is ON HOLD Authors: Yokoyama, T. Description: Crystal structure of DAPK1 in complex with isorhapontigenin Category: Unreleased Structures ...

OCA — Wed, 22 Feb 2023 10:40:32 GMT

New page: '''Unreleased structure''' The entry 8ie8 is ON HOLD Authors: Yokoyama, T. Description: Crystal structure of DAPK1 in complex with isorhapontigenin Category: Unreleased Structures ...

New page

'''Unreleased structure'''

The entry 8ie8 is ON HOLD

Authors: Yokoyama, T.

Description: Crystal structure of DAPK1 in complex with isorhapontigenin
[[Category: Unreleased Structures]]
[[Category: Yokoyama, T]]