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Casein kinase I isoform delta (CKI-delta) (EC 2.7.11.1) (Tau-protein kinase CSNK1D) (EC 2.7.11.26)

 KC1D_RAT                Reviewed;         415 AA.
Q06486; Q99KK4;
01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
10-MAY-2004, sequence version 2.
05-DEC-2018, entry version 168.
RecName: Full=Casein kinase I isoform delta;
Short=CKI-delta;
EC=2.7.11.1;
AltName: Full=Tau-protein kinase CSNK1D;
EC=2.7.11.26;
Name=Csnk1d; Synonyms=Hckid;
Rattus norvegicus (Rat).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Rattus.
NCBI_TaxID=10116;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), AND PROTEIN SEQUENCE OF 1-6.
TISSUE=Testis;
PubMed=8454611;
Graves P.R., Haas D.W., Hagedorn C.H., Depaoli-Roach A.A., Roach P.J.;
"Molecular cloning, expression, and characterization of a 49-
kilodalton casein kinase I isoform from rat testis.";
J. Biol. Chem. 268:6394-6401(1993).
[2]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Takano A., Nagai K.;
"Casein kinase 1 delta rat.";
Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases.
[3]
AUTOPHOSPHORYLATION, AND AUTOINHIBITORY DOMAIN.
PubMed=7665585; DOI=10.1074/jbc.270.37.21689;
Graves P.R., Roach P.J.;
"Role of COOH-terminal phosphorylation in the regulation of casein
kinase I delta.";
J. Biol. Chem. 270:21689-21694(1995).
[4]
TISSUE SPECIFICITY.
PubMed=11165242; DOI=10.1016/S0014-5793(00)02434-0;
Camacho F., Cilio M., Guo Y., Virshup D.M., Patel K., Khorkova O.,
Styren S., Morse B., Yao Z., Keesler G.A.;
"Human casein kinase Idelta phosphorylation of human circadian clock
proteins period 1 and 2.";
FEBS Lett. 489:159-165(2001).
[5]
FUNCTION AS MAP1A KINASE, AND INTERACTION WITH MAP1A.
PubMed=15961172; DOI=10.1016/j.bbamcr.2005.05.004;
Wolff S., Xiao Z., Wittau M., Suessner N., Stoeter M., Knippschild U.;
"Interaction of casein kinase 1 delta (CK1 delta) with the light chain
LC2 of microtubule associated protein 1A (MAP1A).";
Biochim. Biophys. Acta 1745:196-206(2005).
[6]
PHOSPHORYLATION AT SER-370 BY PKA.
PubMed=17594292; DOI=10.1042/BJ20070091;
Giamas G., Hirner H., Shoshiashvili L., Grothey A., Gessert S.,
Kuehl M., Henne-Bruns D., Vorgias C.E., Knippschild U.;
"Phosphorylation of CK1delta: identification of Ser370 as the major
phosphorylation site targeted by PKA in vitro and in vivo.";
Biochem. J. 406:389-398(2007).
[7]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-382, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22673903; DOI=10.1038/ncomms1871;
Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A.,
Lundby C., Olsen J.V.;
"Quantitative maps of protein phosphorylation sites across 14
different rat organs and tissues.";
Nat. Commun. 3:876-876(2012).
[8]
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-317, AND ACTIVE SITE.
PubMed=8648628; DOI=10.1006/jmbi.1996.0189;
Longenecker K.L., Roach P.J., Hurley T.D.;
"Three-dimensional structure of mammalian casein kinase I: molecular
basis for phosphate recognition.";
J. Mol. Biol. 257:618-631(1996).
-!- FUNCTION: 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. In balance with PP1, determines
the circadian period length through the regulation of the speed
and rhythmicity of PER1 and PER2 phosphorylation. Controls PER1
and PER2 nuclear transport and degradation. 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 (By similarity). {ECO:0000250,
ECO:0000269|PubMed:15961172}.
-!- CATALYTIC ACTIVITY:
Reaction=ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-
[protein]; Xref=Rhea:RHEA:17989, Rhea:RHEA-COMP:9863, Rhea:RHEA-
COMP:11604, ChEBI:CHEBI:15378, ChEBI:CHEBI:29999,
ChEBI:CHEBI:30616, ChEBI:CHEBI:83421, ChEBI:CHEBI:456216;
EC=2.7.11.1;
-!- CATALYTIC ACTIVITY:
Reaction=ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-
threonyl-[protein]; Xref=Rhea:RHEA:46608, Rhea:RHEA-COMP:11060,
Rhea:RHEA-COMP:11605, ChEBI:CHEBI:15378, ChEBI:CHEBI:30013,
ChEBI:CHEBI:30616, ChEBI:CHEBI:61977, ChEBI:CHEBI:456216;
EC=2.7.11.1;
-!- CATALYTIC ACTIVITY:
Reaction=[tau protein]-L-serine + ATP = [tau protein]-O-phospho-L-
serine + ADP + H(+); Xref=Rhea:RHEA:12801, Rhea:RHEA-COMP:13701,
Rhea:RHEA-COMP:13702, ChEBI:CHEBI:15378, ChEBI:CHEBI:29999,
ChEBI:CHEBI:30616, ChEBI:CHEBI:83421, ChEBI:CHEBI:456216;
EC=2.7.11.26;
-!- CATALYTIC ACTIVITY:
Reaction=[tau protein]-L-threonine + ATP = [tau protein]-O-
phospho-L-threonine + ADP + H(+); Xref=Rhea:RHEA:53904,
Rhea:RHEA-COMP:13703, Rhea:RHEA-COMP:13704, ChEBI:CHEBI:15378,
ChEBI:CHEBI:30013, ChEBI:CHEBI:30616, ChEBI:CHEBI:61977,
ChEBI:CHEBI:456216; EC=2.7.11.26;
-!- ACTIVITY REGULATION: Drug-mediated inhibition leads to a delay of
the oscillations with the magnitude of this effect dependent upon
the timing of drug administration. Inhibited by phosphorylation
(By similarity). Exhibits substrate-dependent heparin activation.
{ECO:0000250}.
-!- SUBUNIT: Binds to DNMT1. Monomer. Component of the circadian core
oscillator, which includes the CRY proteins, CLOCK, or NPAS2,
ARTNL/BMAL1 or ARTNL2/BMAL2, CSNK1D and/or CSNK1E, TIMELESS and
the PER proteins. Interacts directly with PER1 and PER2 which may
lead to their degradation. Interacts with MAPT/TAU, SNAPIN,
DBNDD2, AIB1/NCOA3 and ESR1. AKAP9/AKAP450 binding promotes
centrosomal subcellular location. Binds to tubulins in mitotic
cells upon DNA damage. Binds to MAP1A.
{ECO:0000269|PubMed:15961172}.
-!- INTERACTION:
Q00987:MDM2 (xeno); NbExp=2; IntAct=EBI-2910316, EBI-389668;
Q9Z266:Snapin (xeno); NbExp=4; IntAct=EBI-7088890, EBI-6170320;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Nucleus
{ECO:0000250}. Cytoplasm, cytoskeleton, microtubule organizing
center, centrosome {ECO:0000250}. Cytoplasm, perinuclear region
{ECO:0000250}. Cell membrane {ECO:0000250}. Cytoplasm,
cytoskeleton, spindle {ECO:0000250}. Golgi apparatus
{ECO:0000250}. Note=Localized at mitotic spindle microtubules, and
at the centrosomes and interphase in interphase cells. Recruited
to the spindle apparatus and the centrosomes in response to DNA-
damage. Correct subcellular localization requires kinase activity
(By similarity). {ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q06486-1; Sequence=Displayed;
Name=2;
IsoId=Q06486-2; Sequence=VSP_010255;
-!- TISSUE SPECIFICITY: Expressed in most tissues, including heart,
brain, testis, kidney, spleen and lung.
{ECO:0000269|PubMed:11165242}.
-!- DOMAIN: The autoinhibitory domain is involved in regulating enzyme
activity through autophosphorylation and possibly, through heparin
binding.
-!- PTM: Autophosphorylated on serine and threonine residues; this
autophosphorylation represses activity. Reactivated by
phosphatase-mediated dephosphorylation. May be dephosphorylated by
PP1. {ECO:0000269|PubMed:17594292}.
-!- SIMILARITY: Belongs to the protein kinase superfamily. CK1 Ser/Thr
protein kinase family. Casein kinase I subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; L07578; AAA40934.1; -; mRNA.
EMBL; AB063114; BAB60852.1; -; mRNA.
PIR; A46002; A46002.
RefSeq; NP_620691.2; NM_139060.3. [Q06486-1]
UniGene; Rn.8046; -.
PDB; 1CKI; X-ray; 2.30 A; A/B=1-317.
PDB; 1CKJ; X-ray; 2.46 A; A/B=1-317.
PDBsum; 1CKI; -.
PDBsum; 1CKJ; -.
ProteinModelPortal; Q06486; -.
SMR; Q06486; -.
BioGrid; 249077; 14.
IntAct; Q06486; 11.
MINT; Q06486; -.
STRING; 10116.ENSRNOP00000015178; -.
BindingDB; Q06486; -.
ChEMBL; CHEMBL4484; -.
iPTMnet; Q06486; -.
PhosphoSitePlus; Q06486; -.
PaxDb; Q06486; -.
PRIDE; Q06486; -.
Ensembl; ENSRNOT00000015178; ENSRNOP00000015178; ENSRNOG00000036676. [Q06486-2]
Ensembl; ENSRNOT00000054936; ENSRNOP00000051819; ENSRNOG00000036676. [Q06486-1]
GeneID; 64462; -.
KEGG; rno:64462; -.
CTD; 1453; -.
RGD; 71031; Csnk1d.
eggNOG; KOG1164; Eukaryota.
eggNOG; ENOG410XPGP; LUCA.
GeneTree; ENSGT00940000153536; -.
HOGENOM; HOG000182055; -.
HOVERGEN; HBG000176; -.
InParanoid; Q06486; -.
KO; K08959; -.
OMA; RWYGTEC; -.
OrthoDB; EOG091G0AFG; -.
PhylomeDB; Q06486; -.
BRENDA; 2.7.11.1; 5301.
Reactome; R-RNO-204005; COPII-mediated vesicle transport.
Reactome; R-RNO-2565942; Regulation of PLK1 Activity at G2/M Transition.
Reactome; R-RNO-380259; Loss of Nlp from mitotic centrosomes.
Reactome; R-RNO-380270; Recruitment of mitotic centrosome proteins and complexes.
Reactome; R-RNO-380320; Recruitment of NuMA to mitotic centrosomes.
Reactome; R-RNO-5620912; Anchoring of the basal body to the plasma membrane.
Reactome; R-RNO-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
Reactome; R-RNO-8854518; AURKA Activation by TPX2.
EvolutionaryTrace; Q06486; -.
PRO; PR:Q06486; -.
Proteomes; UP000002494; Chromosome 10.
Bgee; ENSRNOG00000036676; Expressed in 10 organ(s), highest expression level in testis.
Genevisible; Q06486; RN.
GO; GO:0005813; C:centrosome; IDA:RGD.
GO; GO:0005794; C:Golgi apparatus; IDA:RGD.
GO; GO:0043005; C:neuron projection; IDA:RGD.
GO; GO:0005634; C:nucleus; ISS:UniProtKB.
GO; GO:0048471; C:perinuclear region of cytoplasm; IDA:RGD.
GO; GO:0005886; C:plasma membrane; IDA:RGD.
GO; GO:0005876; C:spindle microtubule; IBA:GO_Central.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0016301; F:kinase activity; IDA:RGD.
GO; GO:0042277; F:peptide binding; IDA:RGD.
GO; GO:0004672; F:protein kinase activity; ISS:UniProtKB.
GO; GO:0004674; F:protein serine/threonine kinase activity; IDA:RGD.
GO; GO:0050321; F:tau-protein kinase activity; IEA:UniProtKB-EC.
GO; GO:1990090; P:cellular response to nerve growth factor stimulus; IEP:RGD.
GO; GO:0032922; P:circadian regulation of gene expression; ISS:UniProtKB.
GO; GO:0007030; P:Golgi organization; IEA:Ensembl.
GO; GO:0007020; P:microtubule nucleation; IEA:Ensembl.
GO; GO:1905515; P:non-motile cilium assembly; IBA:GO_Central.
GO; GO:0018105; P:peptidyl-serine phosphorylation; IBA:GO_Central.
GO; GO:0018107; P:peptidyl-threonine phosphorylation; IBA:GO_Central.
GO; GO:0090263; P:positive regulation of canonical Wnt signaling pathway; IBA:GO_Central.
GO; GO:2000052; P:positive regulation of non-canonical Wnt signaling pathway; IEA:Ensembl.
GO; GO:0032436; P:positive regulation of proteasomal ubiquitin-dependent protein catabolic process; ISS:UniProtKB.
GO; GO:0001934; P:positive regulation of protein phosphorylation; IEA:Ensembl.
GO; GO:0071539; P:protein localization to centrosome; IEA:Ensembl.
GO; GO:0061512; P:protein localization to cilium; IEA:Ensembl.
GO; GO:0034067; P:protein localization to Golgi apparatus; IEA:Ensembl.
GO; GO:0006468; P:protein phosphorylation; IDA:RGD.
GO; GO:0042752; P:regulation of circadian rhythm; ISS:UniProtKB.
GO; GO:0051225; P:spindle assembly; IBA:GO_Central.
GO; GO:0016055; P:Wnt signaling pathway; IEA:UniProtKB-KW.
InterPro; IPR011009; Kinase-like_dom_sf.
InterPro; IPR000719; Prot_kinase_dom.
InterPro; IPR017441; Protein_kinase_ATP_BS.
InterPro; IPR008271; Ser/Thr_kinase_AS.
Pfam; PF00069; Pkinase; 1.
SMART; SM00220; S_TKc; 1.
SUPFAM; SSF56112; SSF56112; 1.
PROSITE; PS00107; PROTEIN_KINASE_ATP; 1.
PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
PROSITE; PS00108; PROTEIN_KINASE_ST; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; ATP-binding; Biological rhythms;
Cell membrane; Complete proteome; Cytoplasm; Cytoskeleton;
Direct protein sequencing; Golgi apparatus; Kinase; Membrane;
Methylation; Nucleotide-binding; Nucleus; Phosphoprotein;
Reference proteome; Serine/threonine-protein kinase; Transferase;
Wnt signaling pathway.
CHAIN 1 415 Casein kinase I isoform delta.
/FTId=PRO_0000192836.
DOMAIN 9 277 Protein kinase. {ECO:0000255|PROSITE-
ProRule:PRU00159}.
NP_BIND 15 23 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00159}.
REGION 278 364 Centrosomal localization signal (CLS).
{ECO:0000250}.
REGION 317 342 Autoinhibitory.
ACT_SITE 128 128 Proton acceptor. {ECO:0000255|PROSITE-
ProRule:PRU00159, ECO:0000255|PROSITE-
ProRule:PRU10027,
ECO:0000269|PubMed:8648628}.
BINDING 38 38 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00159}.
MOD_RES 328 328 Phosphoserine.
{ECO:0000250|UniProtKB:P48730}.
MOD_RES 331 331 Phosphoserine.
{ECO:0000250|UniProtKB:P48730}.
MOD_RES 370 370 Phosphoserine; by PKA.
{ECO:0000269|PubMed:17594292}.
MOD_RES 375 375 Omega-N-methylarginine.
{ECO:0000250|UniProtKB:Q9DC28}.
MOD_RES 382 382 Phosphoserine.
{ECO:0000244|PubMed:22673903}.
MOD_RES 383 383 Phosphoserine.
{ECO:0000250|UniProtKB:P48730}.
MOD_RES 384 384 Phosphoserine.
{ECO:0000250|UniProtKB:P48730}.
MOD_RES 407 407 Phosphoserine.
{ECO:0000250|UniProtKB:P48730}.
MOD_RES 411 411 Phosphoserine.
{ECO:0000250|UniProtKB:P48730}.
VAR_SEQ 400 415 IPGRVASSGLQSVVHR -> RSRDMASLRLHAARQGARCRP
QRPRRTTY (in isoform 2).
{ECO:0000303|PubMed:8454611}.
/FTId=VSP_010255.
TURN 6 8 {ECO:0000244|PDB:1CKI}.
STRAND 9 17 {ECO:0000244|PDB:1CKI}.
STRAND 19 28 {ECO:0000244|PDB:1CKI}.
TURN 29 31 {ECO:0000244|PDB:1CKI}.
STRAND 34 42 {ECO:0000244|PDB:1CKI}.
HELIX 49 58 {ECO:0000244|PDB:1CKI}.
STRAND 68 74 {ECO:0000244|PDB:1CKI}.
STRAND 77 83 {ECO:0000244|PDB:1CKI}.
HELIX 89 95 {ECO:0000244|PDB:1CKI}.
TURN 96 98 {ECO:0000244|PDB:1CKI}.
HELIX 102 121 {ECO:0000244|PDB:1CKI}.
HELIX 131 133 {ECO:0000244|PDB:1CKI}.
STRAND 134 136 {ECO:0000244|PDB:1CKI}.
HELIX 139 141 {ECO:0000244|PDB:1CKI}.
STRAND 145 147 {ECO:0000244|PDB:1CKI}.
TURN 159 161 {ECO:0000244|PDB:1CKI}.
STRAND 177 179 {ECO:0000244|PDB:1CKI}.
HELIX 182 185 {ECO:0000244|PDB:1CKI}.
HELIX 192 208 {ECO:0000244|PDB:1CKI}.
STRAND 220 222 {ECO:0000244|PDB:1CKJ}.
HELIX 225 234 {ECO:0000244|PDB:1CKI}.
HELIX 237 240 {ECO:0000244|PDB:1CKI}.
TURN 241 243 {ECO:0000244|PDB:1CKI}.
HELIX 246 257 {ECO:0000244|PDB:1CKI}.
HELIX 266 279 {ECO:0000244|PDB:1CKI}.
HELIX 289 292 {ECO:0000244|PDB:1CKI}.
HELIX 293 295 {ECO:0000244|PDB:1CKI}.
SEQUENCE 415 AA; 47316 MW; B97F04AF9EB466D2 CRC64;
MELRVGNRYR LGRKIGSGSF GDIYLGTDIA AGEEVAIKLE CVKTKHPQLH IESKIYKMMQ
GGVGIPTIRW CGAEGDYNVM VMELLGPSLE DLFNFCSRKF SLKTVLLLAD QMISRIEYIH
SKNFIHRDVK PDNFLMGLGK KGNLVYIIDF GLAKKYRDAR THQHIPYREN KNLTGTARYA
SINTHLGIEQ SRRDDLESLG YVLMYFNLGS LPWQGLKAAT KRQKYERISE KKMSTPIEVL
CKGYPSEFAT YLNFCRSLRF DDKPDYSYLR QLFRNLFHRQ GFSYDYVFDW NMLKFGASRA
ADDAERERRD REERLRHSRN PATRGLPSTA SGRLRGTQEV APPTPLTPTS HTANTSPRPV
SGMERERKVS MRLHRGAPVN VSSSDLTGRQ DTSRMSTSQI PGRVASSGLQ SVVHR


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