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[[Image:1ig1.gif|left|200px]]<br /><applet load="1ig1" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1ig1, resolution 1.80&Aring;" />
'''1.8A X-Ray structure of ternary complex of a catalytic domain of death-associated protein kinase with ATP analogue and Mn.'''<br />


==Overview==
==1.8A X-Ray structure of ternary complex of a catalytic domain of death-associated protein kinase with ATP analogue and Mn.==
We have determined X-ray crystal structures with up to 1.5 A resolution of the catalytic domain of death-associated protein kinase (DAPK), the first described member of a novel family of pro-apoptotic and tumor-suppressive serine/threonine kinases. The geometry of the active site was studied in the apo form, in a complex with nonhydrolyzable AMPPnP and in a ternary complex consisting of kinase, AMPPnP and either Mg2+ or Mn2+. The structures revealed a previously undescribed water-mediated stabilization of the interaction between the lysine that is conserved in protein kinases and the beta- and gamma-phosphates of ATP, as well as conformational changes at the active site upon ion binding. Comparison between these structures and nucleotide triphosphate complexes of several other kinases disclosed a number of unique features of the DAPK catalytic domain, among which is a highly ordered basic loop in the N-terminal domain that may participate in enzyme regulation.
<StructureSection load='1ig1' size='340' side='right'caption='[[1ig1]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ig1]] 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=1IG1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IG1 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]] 1.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=1ig1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ig1 OCA], [https://pdbe.org/1ig1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ig1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ig1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ig1 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>
== 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/ig/1ig1_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1ig1 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1IG1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=MN:'>MN</scene> and <scene name='pdbligand=ANP:'>ANP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IG1 OCA].
*[[Death-associated protein kinase 3D structures|Death-associated protein kinase 3D structures]]
 
== References ==
==Reference==
<references/>
Crystal structures of the catalytic domain of human protein kinase associated with apoptosis and tumor suppression., Tereshko V, Teplova M, Brunzelle J, Watterson DM, Egli M, Nat Struct Biol. 2001 Oct;8(10):899-907. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11573098 11573098]
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Brunzelle, J.]]
[[Category: Brunzelle J]]
[[Category: Egli, M.]]
[[Category: Egli M]]
[[Category: Teplova, M.]]
[[Category: Teplova M]]
[[Category: Tereshko, V.]]
[[Category: Tereshko V]]
[[Category: Watterson, D M.]]
[[Category: Watterson DM]]
[[Category: ANP]]
[[Category: MN]]
[[Category: transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:11:30 2008''

Latest revision as of 10:35, 7 February 2024

1.8A X-Ray structure of ternary complex of a catalytic domain of death-associated protein kinase with ATP analogue and Mn.1.8A X-Ray structure of ternary complex of a catalytic domain of death-associated protein kinase with ATP analogue and Mn.

Structural highlights

1ig1 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 1.8Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Isoform 2 cannot induce apoptosis but can induce membrane blebbing.[16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30]

Evolutionary Conservation

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

See Also

References

  1. ↑ Deiss LP, Feinstein E, Berissi H, Cohen O, Kimchi A. Identification of a novel serine/threonine kinase and a novel 15-kD protein as potential mediators of the gamma interferon-induced cell death. Genes Dev. 1995 Jan 1;9(1):15-30. PMID:7828849
  2. ↑ Inbal B, Shani G, Cohen O, Kissil JL, Kimchi A. Death-associated protein kinase-related protein 1, a novel serine/threonine kinase involved in apoptosis. Mol Cell Biol. 2000 Feb;20(3):1044-54. PMID:10629061
  3. ↑ Shohat G, Spivak-Kroizman T, Cohen O, Bialik S, Shani G, Berrisi H, Eisenstein M, Kimchi A. The pro-apoptotic function of death-associated protein kinase is controlled by a unique inhibitory autophosphorylation-based mechanism. J Biol Chem. 2001 Dec 14;276(50):47460-7. Epub 2001 Sep 28. PMID:11579085 doi:10.1074/jbc.M105133200
  4. ↑ Inbal B, Bialik S, Sabanay I, Shani G, Kimchi A. DAP kinase and DRP-1 mediate membrane blebbing and the formation of autophagic vesicles during programmed cell death. J Cell Biol. 2002 Apr 29;157(3):455-68. Epub 2002 Apr 29. PMID:11980920 doi:10.1083/jcb.200109094
  5. ↑ Tian JH, Das S, Sheng ZH. Ca2+-dependent phosphorylation of syntaxin-1A by the death-associated protein (DAP) kinase regulates its interaction with Munc18. J Biol Chem. 2003 Jul 11;278(28):26265-74. Epub 2003 May 2. PMID:12730201 doi:10.1074/jbc.M300492200
  6. ↑ 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
  7. ↑ Eisenberg-Lerner A, Kimchi A. DAP kinase regulates JNK signaling by binding and activating protein kinase D under oxidative stress. Cell Death Differ. 2007 Nov;14(11):1908-15. Epub 2007 Aug 17. PMID:17703233 doi:10.1038/sj.cdd.4402212
  8. ↑ Houle F, Poirier A, Dumaresq J, Huot J. DAP kinase mediates the phosphorylation of tropomyosin-1 downstream of the ERK pathway, which regulates the formation of stress fibers in response to oxidative stress. J Cell Sci. 2007 Oct 15;120(Pt 20):3666-77. Epub 2007 Sep 25. PMID:17895359 doi:10.1242/jcs.003251
  9. ↑ Lin Y, Stevens C, Hrstka R, Harrison B, Fourtouna A, Pathuri S, Vojtesek B, Hupp T. An alternative transcript from the death-associated protein kinase 1 locus encoding a small protein selectively mediates membrane blebbing. FEBS J. 2008 May;275(10):2574-84. doi: 10.1111/j.1742-4658.2008.06404.x. Epub, 2008 Apr 15. PMID:18422656 doi:10.1111/j.1742-4658.2008.06404.x
  10. ↑ Harrison B, Kraus M, Burch L, Stevens C, Craig A, Gordon-Weeks P, Hupp TR. DAPK-1 binding to a linear peptide motif in MAP1B stimulates autophagy and membrane blebbing. J Biol Chem. 2008 Apr 11;283(15):9999-10014. doi: 10.1074/jbc.M706040200. Epub, 2008 Jan 14. PMID:18195017 doi:10.1074/jbc.M706040200
  11. ↑ 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
  12. ↑ Zalckvar E, Berissi H, Mizrachy L, Idelchuk Y, Koren I, Eisenstein M, Sabanay H, Pinkas-Kramarski R, Kimchi A. DAP-kinase-mediated phosphorylation on the BH3 domain of beclin 1 promotes dissociation of beclin 1 from Bcl-XL and induction of autophagy. EMBO Rep. 2009 Mar;10(3):285-92. doi: 10.1038/embor.2008.246. Epub 2009 Jan 30. PMID:19180116 doi:10.1038/embor.2008.246
  13. ↑ Stevens C, Lin Y, Harrison B, Burch L, Ridgway RA, Sansom O, Hupp T. Peptide combinatorial libraries identify TSC2 as a death-associated protein kinase (DAPK) death domain-binding protein and reveal a stimulatory role for DAPK in mTORC1 signaling. J Biol Chem. 2009 Jan 2;284(1):334-44. doi: 10.1074/jbc.M805165200. Epub 2008 Oct, 30. PMID:18974095 doi:10.1074/jbc.M805165200
  14. ↑ Lee TH, Chen CH, Suizu F, Huang P, Schiene-Fischer C, Daum S, Zhang YJ, Goate A, Chen RH, Zhou XZ, Lu KP. Death-associated protein kinase 1 phosphorylates Pin1 and inhibits its prolyl isomerase activity and cellular function. Mol Cell. 2011 Apr 22;42(2):147-59. doi: 10.1016/j.molcel.2011.03.005. Epub 2011 , Apr 14. PMID:21497122 doi:10.1016/j.molcel.2011.03.005
  15. ↑ 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
  16. ↑ Deiss LP, Feinstein E, Berissi H, Cohen O, Kimchi A. Identification of a novel serine/threonine kinase and a novel 15-kD protein as potential mediators of the gamma interferon-induced cell death. Genes Dev. 1995 Jan 1;9(1):15-30. PMID:7828849
  17. ↑ Inbal B, Shani G, Cohen O, Kissil JL, Kimchi A. Death-associated protein kinase-related protein 1, a novel serine/threonine kinase involved in apoptosis. Mol Cell Biol. 2000 Feb;20(3):1044-54. PMID:10629061
  18. ↑ Shohat G, Spivak-Kroizman T, Cohen O, Bialik S, Shani G, Berrisi H, Eisenstein M, Kimchi A. The pro-apoptotic function of death-associated protein kinase is controlled by a unique inhibitory autophosphorylation-based mechanism. J Biol Chem. 2001 Dec 14;276(50):47460-7. Epub 2001 Sep 28. PMID:11579085 doi:10.1074/jbc.M105133200
  19. ↑ Inbal B, Bialik S, Sabanay I, Shani G, Kimchi A. DAP kinase and DRP-1 mediate membrane blebbing and the formation of autophagic vesicles during programmed cell death. J Cell Biol. 2002 Apr 29;157(3):455-68. Epub 2002 Apr 29. PMID:11980920 doi:10.1083/jcb.200109094
  20. ↑ Tian JH, Das S, Sheng ZH. Ca2+-dependent phosphorylation of syntaxin-1A by the death-associated protein (DAP) kinase regulates its interaction with Munc18. J Biol Chem. 2003 Jul 11;278(28):26265-74. Epub 2003 May 2. PMID:12730201 doi:10.1074/jbc.M300492200
  21. ↑ 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
  22. ↑ Eisenberg-Lerner A, Kimchi A. DAP kinase regulates JNK signaling by binding and activating protein kinase D under oxidative stress. Cell Death Differ. 2007 Nov;14(11):1908-15. Epub 2007 Aug 17. PMID:17703233 doi:10.1038/sj.cdd.4402212
  23. ↑ Houle F, Poirier A, Dumaresq J, Huot J. DAP kinase mediates the phosphorylation of tropomyosin-1 downstream of the ERK pathway, which regulates the formation of stress fibers in response to oxidative stress. J Cell Sci. 2007 Oct 15;120(Pt 20):3666-77. Epub 2007 Sep 25. PMID:17895359 doi:10.1242/jcs.003251
  24. ↑ Lin Y, Stevens C, Hrstka R, Harrison B, Fourtouna A, Pathuri S, Vojtesek B, Hupp T. An alternative transcript from the death-associated protein kinase 1 locus encoding a small protein selectively mediates membrane blebbing. FEBS J. 2008 May;275(10):2574-84. doi: 10.1111/j.1742-4658.2008.06404.x. Epub, 2008 Apr 15. PMID:18422656 doi:10.1111/j.1742-4658.2008.06404.x
  25. ↑ Harrison B, Kraus M, Burch L, Stevens C, Craig A, Gordon-Weeks P, Hupp TR. DAPK-1 binding to a linear peptide motif in MAP1B stimulates autophagy and membrane blebbing. J Biol Chem. 2008 Apr 11;283(15):9999-10014. doi: 10.1074/jbc.M706040200. Epub, 2008 Jan 14. PMID:18195017 doi:10.1074/jbc.M706040200
  26. ↑ 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
  27. ↑ Zalckvar E, Berissi H, Mizrachy L, Idelchuk Y, Koren I, Eisenstein M, Sabanay H, Pinkas-Kramarski R, Kimchi A. DAP-kinase-mediated phosphorylation on the BH3 domain of beclin 1 promotes dissociation of beclin 1 from Bcl-XL and induction of autophagy. EMBO Rep. 2009 Mar;10(3):285-92. doi: 10.1038/embor.2008.246. Epub 2009 Jan 30. PMID:19180116 doi:10.1038/embor.2008.246
  28. ↑ Stevens C, Lin Y, Harrison B, Burch L, Ridgway RA, Sansom O, Hupp T. Peptide combinatorial libraries identify TSC2 as a death-associated protein kinase (DAPK) death domain-binding protein and reveal a stimulatory role for DAPK in mTORC1 signaling. J Biol Chem. 2009 Jan 2;284(1):334-44. doi: 10.1074/jbc.M805165200. Epub 2008 Oct, 30. PMID:18974095 doi:10.1074/jbc.M805165200
  29. ↑ Lee TH, Chen CH, Suizu F, Huang P, Schiene-Fischer C, Daum S, Zhang YJ, Goate A, Chen RH, Zhou XZ, Lu KP. Death-associated protein kinase 1 phosphorylates Pin1 and inhibits its prolyl isomerase activity and cellular function. Mol Cell. 2011 Apr 22;42(2):147-59. doi: 10.1016/j.molcel.2011.03.005. Epub 2011 , Apr 14. PMID:21497122 doi:10.1016/j.molcel.2011.03.005
  30. ↑ 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

1ig1, resolution 1.80Å

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