2yak: Difference between revisions

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-[[Image:2yak.jpg|left|200px]]
-<!--
+==Structure of death-associated protein Kinase 1 (dapk1) in complex with a ruthenium octasporine ligand (OSV)==
-The line below this paragraph, containing "STRUCTURE_2yak", creates the "Structure Box" on the page.
+<StructureSection load='2yak' size='340' side='right'caption='[[2yak]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2yak]] 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=2YAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YAK FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OSV:RUTHENIUM+OCTASPORINE+4'>OSV</scene></td></tr>
-{{STRUCTURE_2yak|  PDB=2yak  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2yak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yak OCA], [https://pdbe.org/2yak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yak RCSB], [https://www.ebi.ac.uk/pdbsum/2yak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yak 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>
-===STRUCTURE OF DEATH-ASSOCIATED PROTEIN KINASE 1 (DAPK1) IN COMPLEX WITH A RUTHENIUM OCTASPORINE LIGAND (OSV)===
+==See Also==
+*[[Death-associated protein kinase 3D structures|Death-associated protein kinase 3D structures]]
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_21446733}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 21446733 is the PubMed ID number.
+</StructureSection>
--->
-{{ABSTRACT_PUBMED_21446733}}
-==About this Structure==
-[[2yak]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YAK OCA].
-==Reference==
-<ref group="xtra">PMID:21446733</ref><ref group="xtra">PMID:18973295</ref><ref group="xtra">PMID:19035373</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Non-specific serine/threonine protein kinase]]
+[[Category: Large Structures]]
-[[Category: Atilla-Gokcumen, G E.]]
+[[Category: Atilla-Gokcumen GE]]
-[[Category: Blanck, S.]]
+[[Category: Blanck S]]
-[[Category: Celik, M A.]]
+[[Category: Celik MA]]
-[[Category: Essen, L O.]]
+[[Category: Essen L-O]]
-[[Category: Feng, L.]]
+[[Category: Feng L]]
-[[Category: Filippakopoulos, P.]]
+[[Category: Filippakopoulos P]]
-[[Category: Frenking, G.]]
+[[Category: Frenking G]]
-[[Category: Geisselbrecht, Y.]]
+[[Category: Geisselbrecht Y]]
-[[Category: Harms, K.]]
+[[Category: Harms K]]
-[[Category: Knapp, S.]]
+[[Category: Knapp S]]
-[[Category: Kraeling, K.]]
+[[Category: Kraeling K]]
-[[Category: Maksimoska, J.]]
+[[Category: Maksimoska J]]
-[[Category: Marmorstein, R.]]
+[[Category: Marmorstein R]]
-[[Category: Meggers, E.]]
+[[Category: Meggers E]]
-[[Category: Wilbuer, A.]]
+[[Category: Wilbuer A]]