ID KC13_YEAST Reviewed; 524 AA.
AC P39962; D3DM29;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 2.
DT 27-MAR-2024, entry version 199.
DE RecName: Full=Casein kinase I homolog 3;
DE EC=2.7.11.1;
GN Name=YCK3; Synonyms=CKI3; OrderedLocusNames=YER123W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8816449; DOI=10.1128/mcb.16.10.5375;
RA Wang X., Hoekstra M.F., Demaggio A.J., Dhillon N., Vancura A., Kuret J.,
RA Johnston G.C., Singer R.A.;
RT "Prenylated isoforms of yeast casein kinase I, including the novel Yck3p,
RT suppress the gcs1 blockage of cell proliferation from stationary phase.";
RL Mol. Cell. Biol. 16:5375-5385(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [5]
RP PALMITOYLATION AT CYS-517; CYS-518; CYS-519; CYS-520; CYS-522; CYS-523 AND
RP CYS-524, TARGETING SIGNAL, AND MUTAGENESIS OF TYR-444; SER-446 AND ILE-447.
RX PubMed=14668479; DOI=10.1091/mbc.e03-09-0682;
RA Sun B., Chen L., Cao W., Roth A.F., Davis N.G.;
RT "The yeast casein kinase Yck3p is palmitoylated, then sorted to the
RT vacuolar membrane with AP-3-dependent recognition of a YXXPhi adaptin
RT sorting signal.";
RL Mol. Biol. Cell 15:1397-1406(2004).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [8]
RP FUNCTION.
RX PubMed=32391792; DOI=10.7554/elife.56090;
RA Langemeyer L., Borchers A.C., Herrmann E., Fuellbrunn N., Han Y., Perz A.,
RA Auffarth K., Kuemmel D., Ungermann C.;
RT "A conserved and regulated mechanism drives endosomal Rab transition.";
RL Elife 9:0-0(2020).
CC -!- FUNCTION: Casein kinases are operationally defined by their
CC preferential utilization of acidic proteins such as caseins as
CC substrates. Phosphorylates MON1, inhibiting the guanine nucleotide
CC exchange factor activity of the MON1-CCZ1 complex, possibly by
CC preventing its recruitment to membranes by small GTPase RAB5 homologs
CC (PubMed:32391792). {ECO:0000269|PubMed:32391792}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-
CC [protein]; Xref=Rhea:RHEA:17989, Rhea:RHEA-COMP:9863, Rhea:RHEA-
CC COMP:11604, ChEBI:CHEBI:15378, ChEBI:CHEBI:29999, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:83421, ChEBI:CHEBI:456216; EC=2.7.11.1;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-
CC threonyl-[protein]; Xref=Rhea:RHEA:46608, Rhea:RHEA-COMP:11060,
CC Rhea:RHEA-COMP:11605, ChEBI:CHEBI:15378, ChEBI:CHEBI:30013,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:61977, ChEBI:CHEBI:456216;
CC EC=2.7.11.1;
CC -!- SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor; Cytoplasmic side.
CC Nucleus membrane; Lipid-anchor; Cytoplasmic side. Vacuole membrane;
CC Lipid-anchor; Cytoplasmic side. Note=Targeting to the vacuolar membrane
CC may depend on AP-3 pathway.
CC -!- DOMAIN: The YXXZ (Tyr-Xaa-Xaa-Zaa, where Zaa is a hydrophobic residue)
CC motif mediates the targeting to the lysosomal compartments.
CC -!- MISCELLANEOUS: Present with 1320 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the protein kinase superfamily. CK1 Ser/Thr
CC protein kinase family. Casein kinase I subfamily. {ECO:0000305}.
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DR EMBL; X87108; CAA60589.1; -; Genomic_DNA.
DR EMBL; U18916; AAC03221.2; -; Genomic_DNA.
DR EMBL; BK006939; DAA07783.1; -; Genomic_DNA.
DR PIR; S50626; S50626.
DR RefSeq; NP_011049.2; NM_001179013.1.
DR AlphaFoldDB; P39962; -.
DR SMR; P39962; -.
DR BioGRID; 36867; 204.
DR DIP; DIP-6331N; -.
DR IntAct; P39962; 6.
DR MINT; P39962; -.
DR STRING; 4932.YER123W; -.
DR GlyGen; P39962; 5 sites, 1 O-linked glycan (5 sites).
DR iPTMnet; P39962; -.
DR SwissPalm; P39962; -.
DR MaxQB; P39962; -.
DR PaxDb; 4932-YER123W; -.
DR PeptideAtlas; P39962; -.
DR TopDownProteomics; P39962; -.
DR EnsemblFungi; YER123W_mRNA; YER123W; YER123W.
DR GeneID; 856860; -.
DR KEGG; sce:YER123W; -.
DR AGR; SGD:S000000925; -.
DR SGD; S000000925; YCK3.
DR VEuPathDB; FungiDB:YER123W; -.
DR eggNOG; KOG1165; Eukaryota.
DR GeneTree; ENSGT00940000176388; -.
DR HOGENOM; CLU_019279_1_0_1; -.
DR InParanoid; P39962; -.
DR OMA; FEWCGRK; -.
DR OrthoDB; 1534388at2759; -.
DR BioCyc; YEAST:YER123W-MONOMER; -.
DR BRENDA; 2.7.11.1; 984.
DR BioGRID-ORCS; 856860; 2 hits in 13 CRISPR screens.
DR PRO; PR:P39962; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P39962; Protein.
DR GO; GO:0000324; C:fungal-type vacuole; IDA:SGD.
DR GO; GO:0000329; C:fungal-type vacuole membrane; IDA:SGD.
DR GO; GO:0031965; C:nuclear membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0005886; C:plasma membrane; IDA:SGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004672; F:protein kinase activity; HDA:SGD.
DR GO; GO:0106310; F:protein serine kinase activity; IEA:RHEA.
DR GO; GO:0004674; F:protein serine/threonine kinase activity; ISS:SGD.
DR GO; GO:0006897; P:endocytosis; IBA:GO_Central.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0007165; P:signal transduction; IBA:GO_Central.
DR GO; GO:0016192; P:vesicle-mediated transport; IMP:SGD.
DR Gene3D; 1.10.510.10; Transferase(Phosphotransferase) domain 1; 1.
DR InterPro; IPR011009; Kinase-like_dom_sf.
DR InterPro; IPR000719; Prot_kinase_dom.
DR InterPro; IPR008271; Ser/Thr_kinase_AS.
DR PANTHER; PTHR11909; CASEIN KINASE-RELATED; 1.
DR PANTHER; PTHR11909:SF155; GILGAMESH, ISOFORM L; 1.
DR Pfam; PF00069; Pkinase; 1.
DR SMART; SM00220; S_TKc; 1.
DR SUPFAM; SSF56112; Protein kinase-like (PK-like); 1.
DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
DR PROSITE; PS00108; PROTEIN_KINASE_ST; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cell membrane; Kinase; Lipoprotein; Membrane;
KW Nucleotide-binding; Nucleus; Palmitate; Reference proteome;
KW Serine/threonine-protein kinase; Transferase; Vacuole.
FT CHAIN 1..524
FT /note="Casein kinase I homolog 3"
FT /id="PRO_0000192858"
FT DOMAIN 14..319
FT /note="Protein kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT REGION 352..414
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 427..474
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 444..447
FT /note="YXXZ targeting signal"
FT COMPBIAS 357..414
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 150
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159,
FT ECO:0000255|PROSITE-ProRule:PRU10027"
FT BINDING 20..28
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT BINDING 60
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT LIPID 517
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000305|PubMed:14668479"
FT LIPID 518
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000305|PubMed:14668479"
FT LIPID 519
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000305|PubMed:14668479"
FT LIPID 520
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000305|PubMed:14668479"
FT LIPID 522
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000305|PubMed:14668479"
FT LIPID 523
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000305|PubMed:14668479"
FT LIPID 524
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000305|PubMed:14668479"
FT MUTAGEN 444
FT /note="Y->H: Impaired vacuolar targeting."
FT /evidence="ECO:0000269|PubMed:14668479"
FT MUTAGEN 446
FT /note="S->P: Impaired vacuolar targeting."
FT /evidence="ECO:0000269|PubMed:14668479"
FT MUTAGEN 447
FT /note="I->N: Impaired vacuolar targeting."
FT /evidence="ECO:0000269|PubMed:14668479"
SQ SEQUENCE 524 AA; 60261 MW; FD4BBA311D0CD805 CRC64;
MSQRSSQHIV GIHYAVGPKI GEGSFGVIFE GENILHSCQA QTGSKRDSSI IMANEPVAIK
FEPRHSDAPQ LRDEFRAYRI LNGCVGIPHA YYFGQEGMHN ILIIDLLGPS LEDLFEWCGR
KFSVKTTCMV AKQMIDRVRA IHDHDLIYRD IKPDNFLISQ YQRISPEGKV IKSCASSSNN
DPNLIYMVDF GMAKQYRDPR TKQHIPYRER KSLSGTARYM SINTHFGREQ SRRDDLESLG
HVFFYFLRGS LPWQGLKAPN NKLKYEKIGM TKQKLNPDDL LLNNAIPYQF ATYLKYARSL
KFDEDPDYDY LISLMDDALR LNDLKDDGHY DWMDLNGGKG WNIKINRRAN LHGYGNPNPR
VNGNTARNNV NTNSKTRNTT PVATPKQQAQ NSYNKDNSKS RISSNPQSFT KQQHVLKKIE
PNSKYIPETH SNLQRPIKSQ SQTYDSISHT QNSPFVPYSS SKANPKRSNN EHNLPNHYTN
LANKNINYQS QRNYEQENDA YSDDENDTFC SKIYKYCCCC FCCC
//
