3bqr

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with an imidazo-pyridazine ligand

Structural highlights

3bqr is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.75Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] Isoform 2 can phosphorylate myosin, PPP1R12A and MYL12B.^[13] ^[14] ^[15] ^[16] ^[17] ^[18] ^[19] ^[20] ^[21] ^[22] ^[23] ^[24]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Murata-Hori M, Suizu F, Iwasaki T, Kikuchi A, Hosoya H. ZIP kinase identified as a novel myosin regulatory light chain kinase in HeLa cells. FEBS Lett. 1999 May 14;451(1):81-4. PMID:10356987
↑ Takamoto N, Komatsu S, Komaba S, Niiro N, Ikebe M. Novel ZIP kinase isoform lacks leucine zipper. Arch Biochem Biophys. 2006 Dec 15;456(2):194-203. Epub 2006 Oct 16. PMID:17126281 doi:S0003-9861(06)00373-0
↑ Kawai T, Akira S, Reed JC. ZIP kinase triggers apoptosis from nuclear PML oncogenic domains. Mol Cell Biol. 2003 Sep;23(17):6174-86. PMID:12917339
↑ Preuss U, Landsberg G, Scheidtmann KH. Novel mitosis-specific phosphorylation of histone H3 at Thr11 mediated by Dlk/ZIP kinase. Nucleic Acids Res. 2003 Feb 1;31(3):878-85. PMID:12560483
↑ Shani G, Marash L, Gozuacik D, Bialik S, Teitelbaum L, Shohat G, Kimchi A. Death-associated protein kinase phosphorylates ZIP kinase, forming a unique kinase hierarchy to activate its cell death functions. Mol Cell Biol. 2004 Oct;24(19):8611-26. PMID:15367680 doi:10.1128/MCB.24.19.8611-8626.2004
↑ Mukhopadhyay R, Ray PS, Arif A, Brady AK, Kinter M, Fox PL. DAPK-ZIPK-L13a axis constitutes a negative-feedback module regulating inflammatory gene expression. Mol Cell. 2008 Nov 7;32(3):371-82. doi: 10.1016/j.molcel.2008.09.019. PMID:18995835 doi:10.1016/j.molcel.2008.09.019
↑ Sato N, Kawai T, Sugiyama K, Muromoto R, Imoto S, Sekine Y, Ishida M, Akira S, Matsuda T. Physical and functional interactions between STAT3 and ZIP kinase. Int Immunol. 2005 Dec;17(12):1543-52. Epub 2005 Oct 11. PMID:16219639 doi:10.1093/intimm/dxh331
↑ Hagerty L, Weitzel DH, Chambers J, Fortner CN, Brush MH, Loiselle D, Hosoya H, Haystead TA. ROCK1 phosphorylates and activates zipper-interacting protein kinase. J Biol Chem. 2007 Feb 16;282(7):4884-93. Epub 2006 Dec 8. PMID:17158456 doi:10.1074/jbc.M609990200
↑ Ohbayashi N, Okada K, Kawakami S, Togi S, Sato N, Ikeda O, Kamitani S, Muromoto R, Sekine Y, Kawai T, Akira S, Matsuda T. Physical and functional interactions between ZIP kinase and UbcH5. Biochem Biophys Res Commun. 2008 Aug 8;372(4):708-12. doi:, 10.1016/j.bbrc.2008.05.113. Epub 2008 Jun 2. PMID:18515077 doi:10.1016/j.bbrc.2008.05.113
↑ Leister P, Felten A, Chasan AI, Scheidtmann KH. ZIP kinase plays a crucial role in androgen receptor-mediated transcription. Oncogene. 2008 May 22;27(23):3292-300. Epub 2007 Dec 17. PMID:18084323 doi:10.1038/sj.onc.1210995
↑ Togi S, Ikeda O, Kamitani S, Nakasuji M, Sekine Y, Muromoto R, Nanbo A, Oritani K, Kawai T, Akira S, Matsuda T. Zipper-interacting protein kinase (ZIPK) modulates canonical Wnt/beta-catenin signaling through interaction with Nemo-like kinase and T-cell factor 4 (NLK/TCF4). J Biol Chem. 2011 May 27;286(21):19170-7. doi: 10.1074/jbc.M110.189829. Epub 2011, Mar 30. PMID:21454679 doi:10.1074/jbc.M110.189829
↑ Shoval Y, Berissi H, Kimchi A, Pietrokovski S. New modularity of DAP-kinases: alternative splicing of the DRP-1 gene produces a ZIPk-like isoform. PLoS One. 2011 Mar 8;6(2):e17344. doi: 10.1371/journal.pone.0017344. PMID:21408167 doi:10.1371/journal.pone.0017344
↑ Murata-Hori M, Suizu F, Iwasaki T, Kikuchi A, Hosoya H. ZIP kinase identified as a novel myosin regulatory light chain kinase in HeLa cells. FEBS Lett. 1999 May 14;451(1):81-4. PMID:10356987
↑ Takamoto N, Komatsu S, Komaba S, Niiro N, Ikebe M. Novel ZIP kinase isoform lacks leucine zipper. Arch Biochem Biophys. 2006 Dec 15;456(2):194-203. Epub 2006 Oct 16. PMID:17126281 doi:S0003-9861(06)00373-0
↑ Kawai T, Akira S, Reed JC. ZIP kinase triggers apoptosis from nuclear PML oncogenic domains. Mol Cell Biol. 2003 Sep;23(17):6174-86. PMID:12917339
↑ Preuss U, Landsberg G, Scheidtmann KH. Novel mitosis-specific phosphorylation of histone H3 at Thr11 mediated by Dlk/ZIP kinase. Nucleic Acids Res. 2003 Feb 1;31(3):878-85. PMID:12560483
↑ Shani G, Marash L, Gozuacik D, Bialik S, Teitelbaum L, Shohat G, Kimchi A. Death-associated protein kinase phosphorylates ZIP kinase, forming a unique kinase hierarchy to activate its cell death functions. Mol Cell Biol. 2004 Oct;24(19):8611-26. PMID:15367680 doi:10.1128/MCB.24.19.8611-8626.2004
↑ Mukhopadhyay R, Ray PS, Arif A, Brady AK, Kinter M, Fox PL. DAPK-ZIPK-L13a axis constitutes a negative-feedback module regulating inflammatory gene expression. Mol Cell. 2008 Nov 7;32(3):371-82. doi: 10.1016/j.molcel.2008.09.019. PMID:18995835 doi:10.1016/j.molcel.2008.09.019
↑ Sato N, Kawai T, Sugiyama K, Muromoto R, Imoto S, Sekine Y, Ishida M, Akira S, Matsuda T. Physical and functional interactions between STAT3 and ZIP kinase. Int Immunol. 2005 Dec;17(12):1543-52. Epub 2005 Oct 11. PMID:16219639 doi:10.1093/intimm/dxh331
↑ Hagerty L, Weitzel DH, Chambers J, Fortner CN, Brush MH, Loiselle D, Hosoya H, Haystead TA. ROCK1 phosphorylates and activates zipper-interacting protein kinase. J Biol Chem. 2007 Feb 16;282(7):4884-93. Epub 2006 Dec 8. PMID:17158456 doi:10.1074/jbc.M609990200
↑ Ohbayashi N, Okada K, Kawakami S, Togi S, Sato N, Ikeda O, Kamitani S, Muromoto R, Sekine Y, Kawai T, Akira S, Matsuda T. Physical and functional interactions between ZIP kinase and UbcH5. Biochem Biophys Res Commun. 2008 Aug 8;372(4):708-12. doi:, 10.1016/j.bbrc.2008.05.113. Epub 2008 Jun 2. PMID:18515077 doi:10.1016/j.bbrc.2008.05.113
↑ Leister P, Felten A, Chasan AI, Scheidtmann KH. ZIP kinase plays a crucial role in androgen receptor-mediated transcription. Oncogene. 2008 May 22;27(23):3292-300. Epub 2007 Dec 17. PMID:18084323 doi:10.1038/sj.onc.1210995
↑ Togi S, Ikeda O, Kamitani S, Nakasuji M, Sekine Y, Muromoto R, Nanbo A, Oritani K, Kawai T, Akira S, Matsuda T. Zipper-interacting protein kinase (ZIPK) modulates canonical Wnt/beta-catenin signaling through interaction with Nemo-like kinase and T-cell factor 4 (NLK/TCF4). J Biol Chem. 2011 May 27;286(21):19170-7. doi: 10.1074/jbc.M110.189829. Epub 2011, Mar 30. PMID:21454679 doi:10.1074/jbc.M110.189829
↑ Shoval Y, Berissi H, Kimchi A, Pietrokovski S. New modularity of DAP-kinases: alternative splicing of the DRP-1 gene produces a ZIPk-like isoform. PLoS One. 2011 Mar 8;6(2):e17344. doi: 10.1371/journal.pone.0017344. PMID:21408167 doi:10.1371/journal.pone.0017344

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3bqr"

@@ Line 3: / Line 3: @@
 <StructureSection load='3bqr' size='340' side='right'caption='[[3bqr]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bqr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BQR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bqr]] 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=3BQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BQR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4RB:4-(6-{[(1R)-1-(HYDROXYMETHYL)PROPYL]AMINO}IMIDAZO[1,2-B]PYRIDAZIN-3-YL)BENZOIC+ACID'>4RB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</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]] 1.75&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DAPK3, ZIPK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4RB:4-(6-{[(1R)-1-(HYDROXYMETHYL)PROPYL]AMINO}IMIDAZO[1,2-B]PYRIDAZIN-3-YL)BENZOIC+ACID'>4RB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </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=3bqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bqr OCA], [https://pdbe.org/3bqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bqr RCSB], [https://www.ebi.ac.uk/pdbsum/3bqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bqr 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>
+[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]]
@@ Line 28: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Non-specific serine/threonine protein kinase]]
+[[Category: Arrowsmith CH]]
-[[Category: Arrowsmith, C H]]
+[[Category: Edwards AM]]
-[[Category: Delft, F von]]
+[[Category: Fedorov O]]
-[[Category: Edwards, A M]]
+[[Category: Filippakopoulos P]]
-[[Category: Fedorov, O]]
+[[Category: Knapp S]]
-[[Category: Filippakopoulos, P]]
+[[Category: Niesen F]]
-[[Category: Knapp, S]]
+[[Category: Pike ACW]]
-[[Category: Niesen, F]]
+[[Category: Pilka ES]]
-[[Category: Pike, A C.W]]
+[[Category: Rellos P]]
-[[Category: Pilka, E S]]
+[[Category: Weigelt J]]
-[[Category: Rellos, P]]
+[[Category: Von Delft F]]
-[[Category: Structural genomic]]
-[[Category: Weigelt, J]]
-[[Category: Apoptosis]]
-[[Category: Atp-binding]]
-[[Category: Chromatin regulator]]
-[[Category: Dap kinase 3]]
-[[Category: Dap like kinase]]
-[[Category: Dapk3]]
-[[Category: Death associated kinase]]
-[[Category: Dlk]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleus]]
-[[Category: Serine/threonine-protein kinase]]
-[[Category: Sgc]]
-[[Category: Transferase]]
-[[Category: Zip kinase]]
-[[Category: Zipk]]

3bqr

From Proteopedia

Current revision

Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with an imidazo-pyridazine ligand

Structural highlights

Function

Evolutionary Conservation

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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