2j90: Difference between revisions

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-[[Image:2j90.png|left|200px]]
-{{STRUCTURE_2j90|  PDB=2j90  |  SCENE=  }}
+==Crystal structure of human ZIP kinase in complex with a tetracyclic pyridone inhibitor (Pyridone 6)==
+<StructureSection load='2j90' size='340' side='right'caption='[[2j90]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2j90]] is a 2 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=2J90 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J90 FirstGlance]. <br>
+</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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IZA:2-TERT-BUTYL-9-FLUORO-3,6-DIHYDRO-7H-BENZ[H]-IMIDAZ[4,5-F]ISOQUINOLINE-7-ONE'>IZA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</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=2j90 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j90 OCA], [https://pdbe.org/2j90 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j90 RCSB], [https://www.ebi.ac.uk/pdbsum/2j90 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j90 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DAPK3_HUMAN DAPK3_HUMAN] Serine/threonine kinase which is involved in the regulation of apoptosis, autophagy, transcription, translation, actin cytoskeleton reorganization, cell motility, smooth muscle contraction, and mitosis, particularly cytokinesis. 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. Regulates myosin phosphorylation in both smooth muscle and non-muscle cells. In smooth muscle, regulates myosin either directly by phosphorylating MYL12B and MYL9 or through inhibition of smooth muscle myosin phosphatase (SMPP1M) via phosphorylation of PPP1R12A, and the inhibition of SMPP1M functions to enhance muscle responsiveness to Ca(2+) and promote a contractile state. Enhances transcription from AR-responsive promoters in a hormone- and kinase-dependent manner. Phosphorylates STAT3 and enhances its transcriptional activity. Positively regulates the canonical Wnt/beta-catenin signaling through interaction with NLK and TCF7L2. Can disrupt the NLK-TCF7L2 complex thereby influencing the phosphorylation of TCF7L2 by NLK. Phosphorylates histone H3 on 'Thr-11' at centromeres during mitosis. Involved in the formation of promyelocytic leukemia protein nuclear body (PML-NB), one of many subnuclear domains in the eukaryotic cell nucleus, and which is involved in oncogenesis and viral infection. Phosphorylates RPL13A on 'Ser-77' upon interferon-gamma activation which is causing RPL13A release from the ribosome, its association with the GAIT complex and its subsequent involvement in transcript-selective translation inhibition.<ref>PMID:10356987</ref> <ref>PMID:17126281</ref> <ref>PMID:12917339</ref> <ref>PMID:12560483</ref> <ref>PMID:15367680</ref> <ref>PMID:18995835</ref> <ref>PMID:16219639</ref> <ref>PMID:17158456</ref> <ref>PMID:18515077</ref> <ref>PMID:18084323</ref> <ref>PMID:21454679</ref> <ref>PMID:21408167</ref>   Isoform 2 can phosphorylate myosin, PPP1R12A and MYL12B.<ref>PMID:10356987</ref> <ref>PMID:17126281</ref> <ref>PMID:12917339</ref> <ref>PMID:12560483</ref> <ref>PMID:15367680</ref> <ref>PMID:18995835</ref> <ref>PMID:16219639</ref> <ref>PMID:17158456</ref> <ref>PMID:18515077</ref> <ref>PMID:18084323</ref> <ref>PMID:21454679</ref> <ref>PMID:21408167</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j9/2j90_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2j90 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Protein kinase autophosphorylation of activation segment residues is a common regulatory mechanism in phosphorylation-dependent signalling cascades. However, the molecular mechanisms that guarantee specific and efficient phosphorylation of these sites have not been elucidated. Here, we report on three novel and diverse protein kinase structures that reveal an exchanged activation segment conformation. This dimeric arrangement results in an active kinase conformation in trans, with activation segment phosphorylation sites in close proximity to the active site of the interacting protomer. Analytical ultracentrifugation and chemical cross-linking confirmed the presence of dimers in solution. Consensus substrate sequences for each kinase showed that the identified activation segment autophosphorylation sites are non-consensus substrate sites. Based on the presented structural and functional data, a model for specific activation segment phosphorylation at non-consensus substrate sites is proposed that is likely to be common to other kinases from diverse subfamilies.
-===CRYSTAL STRUCTURE OF HUMAN ZIP KINASE IN COMPLEX WITH A TETRACYCLIC PYRIDONE INHIBITOR (PYRIDONE 6)===
+Activation segment dimerization: a mechanism for kinase autophosphorylation of non-consensus sites.,Pike AC, Rellos P, Niesen FH, Turnbull A, Oliver AW, Parker SA, Turk BE, Pearl LH, Knapp S EMBO J. 2008 Feb 20;27(4):704-14. Epub 2008 Jan 31. PMID:18239682<ref>PMID:18239682</ref>
-{{ABSTRACT_PUBMED_18239682}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2j90" style="background-color:#fffaf0;"></div>
-[[2j90]] is a 2 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=2J90 OCA].
 ==See Also==
-*[[Death-associated protein kinase|Death-associated protein kinase]]
+*[[Death-associated protein kinase 3D structures|Death-associated protein kinase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018239682</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Non-specific serine/threonine protein kinase]]
+[[Category: Large Structures]]
-[[Category: Arrowsmith, C H.]]
+[[Category: Arrowsmith CH]]
-[[Category: Berridge, G.]]
+[[Category: Berridge G]]
-[[Category: Delft, F Von.]]
+[[Category: Edwards A]]
-[[Category: Edwards, A.]]
+[[Category: Eswaran J]]
-[[Category: Eswaran, J.]]
+[[Category: Fedorov O]]
-[[Category: Fedorov, O.]]
+[[Category: Gileadi O]]
-[[Category: Gileadi, O.]]
+[[Category: Knapp S]]
-[[Category: Knapp, S.]]
+[[Category: Papagrigoriou E]]
-[[Category: Papagrigoriou, E.]]
+[[Category: Pike ACW]]
-[[Category: Pike, A C.W.]]
+[[Category: Savitsky P]]
-[[Category: Savitsky, P.]]
+[[Category: Sundstrom M]]
-[[Category: Sundstrom, M.]]
+[[Category: Turnbull AP]]
-[[Category: Turnbull, A P.]]
+[[Category: Ugochukwa E]]
-[[Category: Ugochukwa, E.]]
+[[Category: Weigelt J]]
-[[Category: Weigelt, J.]]
+[[Category: Von Delft F]]
-[[Category: Apoptosis]]
-[[Category: Atp-binding]]
-[[Category: Chromatin regulator]]
-[[Category: Kinase]]
-[[Category: Muscle]]
-[[Category: Myosin phosphorylation]]
-[[Category: Nuclear protein]]
-[[Category: Nucleotide-binding]]
-[[Category: Serine/threonine- protein kinase]]
-[[Category: Transferase]]