5x17

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of murine CK1d in complex with ADP

Structural highlights

5x17 is a 2 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KC1D_MOUSE Essential serine/threonine-protein kinase that regulates diverse cellular growth and survival processes including Wnt signaling, DNA repair and circadian rhythms. It can phosphorylate a large number of proteins. Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. Phosphorylates connexin-43/GJA1, MAP1A, SNAPIN, MAPT/TAU, TOP2A, DCK, HIF1A, EIF6, p53/TP53, DVL2, DVL3, ESR1, AIB1/NCOA3, DNMT1, PKD2, YAP1, PER1 and PER2. Central component of the circadian clock. May act as a negative regulator of circadian rhythmicity by phosphorylating PER1 and PER2, leading to retain PER1 in the cytoplasm. YAP1 phosphorylation promotes its SCF(beta-TRCP) E3 ubiquitin ligase-mediated ubiquitination and subsequent degradation. DNMT1 phosphorylation reduces its DNA-binding activity. Phosphorylation of ESR1 and AIB1/NCOA3 stimulates their activity and coactivation. Phosphorylation of DVL2 and DVL3 regulates WNT3A signaling pathway that controls neurite outgrowth. EIF6 phosphorylation promotes its nuclear export. Triggers down-regulation of dopamine receptors in the forebrain. Activates DCK in vitro by phosphorylation. TOP2A phosphorylation favors DNA cleavable complex formation. May regulate the formation of the mitotic spindle apparatus in extravillous trophoblast. Modulates connexin-43/GJA1 gap junction assembly by phosphorylation. Probably involved in lymphocyte physiology. Regulates fast synaptic transmission mediated by glutamate.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

Temperature compensation is a striking feature of the circadian clock. Here we investigate biochemical mechanisms underlying temperature-compensated, CKIdelta-dependent multi-site phosphorylation in mammals. We identify two mechanisms for temperature-insensitive phosphorylation at higher temperature: lower substrate affinity to CKIdelta-ATP complex and higher product affinity to CKIdelta-ADP complex. Inhibitor screening of ADP-dependent phosphatase activity of CKIdelta identified aurintricarboxylic acid (ATA) as a temperature-sensitive kinase activator. Docking simulation of ATA and mutagenesis experiment revealed K224D/K224E mutations in CKIdelta that impaired product binding and temperature-compensated primed phosphorylation. Importantly, K224D mutation shortens behavioral circadian rhythms and changes the temperature dependency of SCN's circadian period. Interestingly, temperature-compensated phosphorylation was evolutionary conserved in yeast. Molecular dynamics simulation and X-ray crystallography demonstrate that an evolutionally conserved CKI-specific domain around K224 can provide a structural basis for temperature-sensitive substrate and product binding. Surprisingly, this domain can confer temperature compensation on a temperature-sensitive TTBK1. These findings suggest the temperature-sensitive substrate- and product-binding mechanisms underlie temperature compensation.

Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock.,Shinohara Y, Koyama YM, Ukai-Tadenuma M, Hirokawa T, Kikuchi M, Yamada RG, Ukai H, Fujishima H, Umehara T, Tainaka K, Ueda HR Mol Cell. 2017 Sep 7;67(5):783-798.e20. doi: 10.1016/j.molcel.2017.08.009. PMID:28886336^[8]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Chergui K, Svenningsson P, Greengard P. Physiological role for casein kinase 1 in glutamatergic synaptic transmission. J Neurosci. 2005 Jul 13;25(28):6601-9. PMID:16014721 doi:10.1523/JNEUROSCI.1082-05.2005
↑ Wolff S, Stoter M, Giamas G, Piesche M, Henne-Bruns D, Banting G, Knippschild U. Casein kinase 1 delta (CK1delta) interacts with the SNARE associated protein snapin. FEBS Lett. 2006 Nov 27;580(27):6477-84. Epub 2006 Nov 7. PMID:17101137 doi:10.1016/j.febslet.2006.10.068
↑ Etchegaray JP, Machida KK, Noton E, Constance CM, Dallmann R, Di Napoli MN, DeBruyne JP, Lambert CM, Yu EA, Reppert SM, Weaver DR. Casein kinase 1 delta regulates the pace of the mammalian circadian clock. Mol Cell Biol. 2009 Jul;29(14):3853-66. doi: 10.1128/MCB.00338-09. Epub 2009 May , 4. PMID:19414593 doi:10.1128/MCB.00338-09
↑ Lee H, Chen R, Lee Y, Yoo S, Lee C. Essential roles of CKIdelta and CKIepsilon in the mammalian circadian clock. Proc Natl Acad Sci U S A. 2009 Dec 15;106(50):21359-64. doi:, 10.1073/pnas.0906651106. Epub 2009 Nov 30. PMID:19948962 doi:10.1073/pnas.0906651106
↑ Sugiyama Y, Hatano N, Sueyoshi N, Suetake I, Tajima S, Kinoshita E, Kinoshita-Kikuta E, Koike T, Kameshita I. The DNA-binding activity of mouse DNA methyltransferase 1 is regulated by phosphorylation with casein kinase 1delta/epsilon. Biochem J. 2010 Apr 14;427(3):489-97. doi: 10.1042/BJ20091856. PMID:20192920 doi:10.1042/BJ20091856
↑ Etchegaray JP, Yu EA, Indic P, Dallmann R, Weaver DR. Casein kinase 1 delta (CK1delta) regulates period length of the mouse suprachiasmatic circadian clock in vitro. PLoS One. 2010 Apr 22;5(4):e10303. doi: 10.1371/journal.pone.0010303. PMID:20421981 doi:10.1371/journal.pone.0010303
↑ Zhou M, Rebholz H, Brocia C, Warner-Schmidt JL, Fienberg AA, Nairn AC, Greengard P, Flajolet M. Forebrain overexpression of CK1delta leads to down-regulation of dopamine receptors and altered locomotor activity reminiscent of ADHD. Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4401-6. doi: 10.1073/pnas.0915173107., Epub 2010 Feb 9. PMID:20145109 doi:10.1073/pnas.0915173107
↑ Shinohara Y, Koyama YM, Ukai-Tadenuma M, Hirokawa T, Kikuchi M, Yamada RG, Ukai H, Fujishima H, Umehara T, Tainaka K, Ueda HR. Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock. Mol Cell. 2017 Sep 7;67(5):783-798.e20. doi: 10.1016/j.molcel.2017.08.009. PMID:28886336 doi:http://dx.doi.org/10.1016/j.molcel.2017.08.009

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5x17"

@@ Line 1: / Line 1: @@
 ==Crystal structure of murine CK1d in complex with ADP==
-<StructureSection load='5x17' size='340' side='right' caption='[[5x17]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='5x17' size='340' side='right'caption='[[5x17]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5x17]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X17 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X17 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5x17]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X17 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X17 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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]] 2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x18|5x18]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5x17 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x17 OCA], [http://pdbe.org/5x17 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x17 RCSB], [http://www.ebi.ac.uk/pdbsum/5x17 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x17 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=5x17 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x17 OCA], [https://pdbe.org/5x17 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x17 RCSB], [https://www.ebi.ac.uk/pdbsum/5x17 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x17 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KC1D_MOUSE KC1D_MOUSE]] Essential serine/threonine-protein kinase that regulates diverse cellular growth and survival processes including Wnt signaling, DNA repair and circadian rhythms. It can phosphorylate a large number of proteins. Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. Phosphorylates connexin-43/GJA1, MAP1A, SNAPIN, MAPT/TAU, TOP2A, DCK, HIF1A, EIF6, p53/TP53, DVL2, DVL3, ESR1, AIB1/NCOA3, DNMT1, PKD2, YAP1, PER1 and PER2. Central component of the circadian clock. May act as a negative regulator of circadian rhythmicity by phosphorylating PER1 and PER2, leading to retain PER1 in the cytoplasm. YAP1 phosphorylation promotes its SCF(beta-TRCP) E3 ubiquitin ligase-mediated ubiquitination and subsequent degradation. DNMT1 phosphorylation reduces its DNA-binding activity. Phosphorylation of ESR1 and AIB1/NCOA3 stimulates their activity and coactivation. Phosphorylation of DVL2 and DVL3 regulates WNT3A signaling pathway that controls neurite outgrowth. EIF6 phosphorylation promotes its nuclear export. Triggers down-regulation of dopamine receptors in the forebrain. Activates DCK in vitro by phosphorylation. TOP2A phosphorylation favors DNA cleavable complex formation. May regulate the formation of the mitotic spindle apparatus in extravillous trophoblast. Modulates connexin-43/GJA1 gap junction assembly by phosphorylation. Probably involved in lymphocyte physiology. Regulates fast synaptic transmission mediated by glutamate.<ref>PMID:16014721</ref> <ref>PMID:17101137</ref> <ref>PMID:19414593</ref> <ref>PMID:19948962</ref> <ref>PMID:20192920</ref> <ref>PMID:20421981</ref> <ref>PMID:20145109</ref>
+[https://www.uniprot.org/uniprot/KC1D_MOUSE KC1D_MOUSE] Essential serine/threonine-protein kinase that regulates diverse cellular growth and survival processes including Wnt signaling, DNA repair and circadian rhythms. It can phosphorylate a large number of proteins. Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. Phosphorylates connexin-43/GJA1, MAP1A, SNAPIN, MAPT/TAU, TOP2A, DCK, HIF1A, EIF6, p53/TP53, DVL2, DVL3, ESR1, AIB1/NCOA3, DNMT1, PKD2, YAP1, PER1 and PER2. Central component of the circadian clock. May act as a negative regulator of circadian rhythmicity by phosphorylating PER1 and PER2, leading to retain PER1 in the cytoplasm. YAP1 phosphorylation promotes its SCF(beta-TRCP) E3 ubiquitin ligase-mediated ubiquitination and subsequent degradation. DNMT1 phosphorylation reduces its DNA-binding activity. Phosphorylation of ESR1 and AIB1/NCOA3 stimulates their activity and coactivation. Phosphorylation of DVL2 and DVL3 regulates WNT3A signaling pathway that controls neurite outgrowth. EIF6 phosphorylation promotes its nuclear export. Triggers down-regulation of dopamine receptors in the forebrain. Activates DCK in vitro by phosphorylation. TOP2A phosphorylation favors DNA cleavable complex formation. May regulate the formation of the mitotic spindle apparatus in extravillous trophoblast. Modulates connexin-43/GJA1 gap junction assembly by phosphorylation. Probably involved in lymphocyte physiology. Regulates fast synaptic transmission mediated by glutamate.<ref>PMID:16014721</ref> <ref>PMID:17101137</ref> <ref>PMID:19414593</ref> <ref>PMID:19948962</ref> <ref>PMID:20192920</ref> <ref>PMID:20421981</ref> <ref>PMID:20145109</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5x17" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Casein kinase 3D structures|Casein kinase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Kikuchi, M]]
+[[Category: Large Structures]]
-[[Category: Shinohara, Y]]
+[[Category: Mus musculus]]
-[[Category: Ueda, H R]]
+[[Category: Kikuchi M]]
-[[Category: Umehara, T]]
+[[Category: Shinohara Y]]
-[[Category: Ck1d]]
+[[Category: Ueda HR]]
-[[Category: Kinase]]
+[[Category: Umehara T]]
-[[Category: Transferase]]

5x17

From Proteopedia

Current revision

Crystal structure of murine CK1d in complex with ADP

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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