HD16N_ORYSJ
ID HD16N_ORYSJ Reviewed; 707 AA.
AC Q852L0;
DT 05-OCT-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=Casein kinase 1-like protein HD16 {ECO:0000305};
DE EC=2.7.11.1 {ECO:0000305};
DE AltName: Full=Os03g0793500 protein {ECO:0000312|EMBL:BAF13445.1};
DE AltName: Full=Protein EARLY FLOWERING 1 {ECO:0000303|PubMed:20400938};
DE AltName: Full=Protein HEADING DATE 16 {ECO:0000303|PubMed:23789941};
GN Name=HD16 {ECO:0000303|PubMed:23789941};
GN Synonyms=CKI {ECO:0000305}, EL1 {ECO:0000303|PubMed:20400938};
GN OrderedLocusNames=Os03g0793500 {ECO:0000312|EMBL:BAF13445.1},
GN LOC_Os03g57940 {ECO:0000312|EMBL:ABF99311.1};
GN ORFNames=OsJ_12923 {ECO:0000312|EMBL:EAZ28883.1},
GN OSJNBb0060J21.12 {ECO:0000312|EMBL:AAO37965.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INTERACTION WITH GHD7 AND SLR1,
RP TISSUE SPECIFICITY, PHOSPHORYLATION, AND POLYMORPHISM.
RC STRAIN=cv. Nipponbare;
RX PubMed=23789941; DOI=10.1111/tpj.12268;
RA Hori K., Ogiso-Tanaka E., Matsubara K., Yamanouchi U., Ebana K., Yano M.;
RT "Hd16, a gene for casein kinase I, is involved in the control of rice
RT flowering time by modulating the day-length response.";
RL Plant J. 76:36-46(2013).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [8]
RP FUNCTION, INTERACTION WITH SLR1, SUBCELLULAR LOCATION, TISSUE SPECIFICITY,
RP DEVELOPMENTAL STAGE, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Zhonghua 11;
RX PubMed=20400938; DOI=10.1038/emboj.2010.75;
RA Dai C., Xue H.W.;
RT "Rice early flowering1, a CKI, phosphorylates DELLA protein SLR1 to
RT negatively regulate gibberellin signalling.";
RL EMBO J. 29:1916-1927(2010).
RN [9]
RP FUNCTION.
RX PubMed=21951842; DOI=10.1111/j.1744-7909.2011.01075.x;
RA Wen B.Q., Xing M.Q., Zhang H., Dai C., Xue H.W.;
RT "Rice homeobox transcription factor HOX1a positively regulates gibberellin
RT responses by directly suppressing EL1.";
RL J. Integr. Plant Biol. 53:869-878(2011).
RN [10]
RP FUNCTION.
RX PubMed=26202549; DOI=10.1186/s12284-015-0058-1;
RA Kwon C.T., Kim S.H., Kim D., Paek N.C.;
RT "The rice floral repressor early flowering1 affects spikelet fertility by
RT modulating gibberellin signaling.";
RL Rice 8:58-58(2015).
CC -!- FUNCTION: Casein kinases are operationally defined by their
CC preferential utilization of acidic proteins such as caseins as
CC substrates. It can phosphorylate a large number of proteins (Probable).
CC Can phosphorylate casein on threonine residues in vitro. Involved in
CC the regulation of flowering time through gibberellin (GA) signaling,
CC and independently of photoperiod. Phosphorylates the DELLA protein
CC SLR1, stabilizing SLR1 protein and sustaining SLR1 activity as
CC repressor of GA signaling (PubMed:20400938). Required for normal
CC development of male floral organs and grains, through modulation of GA
CC signaling (PubMed:26202549). Targeted and repressed by the homeobox
CC protein HAZ1 during GA signaling (PubMed:21951842). Can phosphorylate
CC phosvitin and SLR1 in vitro. Is not required for clock function in
CC either the presence or the absence of light signals. Involved in a
CC genetic control pathway for photoperiodic flowering under long day (LD)
CC conditions that includes HD1, GHD7, HD5 and HD2. Phosphorylates and
CC activates GHD7, a major floral repressor under LD conditions.
CC Phosphorylation of GHD7 enhances its function in the repression of
CC EHD1, HD3A and HD3B/RFT1, and obviously delaying flowering
CC (PubMed:23789941). {ECO:0000269|PubMed:20400938,
CC ECO:0000269|PubMed:21951842, ECO:0000269|PubMed:23789941,
CC ECO:0000269|PubMed:26202549, ECO:0000305}.
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 Evidence={ECO:0000305};
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; Evidence={ECO:0000305};
CC -!- SUBUNIT: Monomer (By similarity). Interacts with GHD7 (via C-terminus)
CC (PubMed:23789941). Interacts with SLR1 (PubMed:20400938,
CC PubMed:23789941). {ECO:0000250|UniProtKB:P48730,
CC ECO:0000269|PubMed:20400938, ECO:0000269|PubMed:23789941}.
CC -!- INTERACTION:
CC Q852L0; Q7G7J6: SLR1; NbExp=2; IntAct=EBI-7913614, EBI-7913631;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P48730}. Nucleus
CC {ECO:0000269|PubMed:20400938}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves and stems
CC (PubMed:20400938). Expressed in leaf vascular bundles, and proximal
CC regions of the shoot and roots (PubMed:23789941).
CC {ECO:0000269|PubMed:20400938, ECO:0000269|PubMed:23789941}.
CC -!- DEVELOPMENTAL STAGE: Specifically expressed at stage 2 during floral
CC development. {ECO:0000269|PubMed:20400938}.
CC -!- INDUCTION: Down-regulated by gibberellin (GA).
CC {ECO:0000269|PubMed:20400938}.
CC -!- PTM: Autophosphorylated. {ECO:0000269|PubMed:23789941}.
CC -!- POLYMORPHISM: The cultivar Koshihikari contains a non-synonymous
CC substitution of Ala-331 to Thr-331, which confers strongly reduced
CC kinase activity of HD16, and results in decreased photoperiod
CC sensitivity compared to the cultivar Nipponbare.
CC {ECO:0000269|PubMed:23789941}.
CC -!- DISRUPTION PHENOTYPE: Early flowering. Enhanced response to gibberellin
CC (GA). {ECO:0000269|PubMed:20400938}.
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; AB753041; BAN15567.1; -; mRNA.
DR EMBL; AC090871; AAO37965.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF99311.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF13445.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS86807.1; -; Genomic_DNA.
DR EMBL; CM000140; EAZ28883.1; -; Genomic_DNA.
DR EMBL; AK121620; BAH00578.1; -; mRNA.
DR RefSeq; XP_015632525.1; XM_015777039.1.
DR RefSeq; XP_015632526.1; XM_015777040.1.
DR RefSeq; XP_015632527.1; XM_015777041.1.
DR AlphaFoldDB; Q852L0; -.
DR SMR; Q852L0; -.
DR IntAct; Q852L0; 1.
DR MINT; Q852L0; -.
DR STRING; 4530.OS03T0793500-01; -.
DR PaxDb; Q852L0; -.
DR PRIDE; Q852L0; -.
DR EnsemblPlants; Os03t0793500-01; Os03t0793500-01; Os03g0793500.
DR EnsemblPlants; Os03t0793500-02; Os03t0793500-02; Os03g0793500.
DR GeneID; 4334396; -.
DR Gramene; Os03t0793500-01; Os03t0793500-01; Os03g0793500.
DR Gramene; Os03t0793500-02; Os03t0793500-02; Os03g0793500.
DR KEGG; osa:4334396; -.
DR eggNOG; KOG1164; Eukaryota.
DR HOGENOM; CLU_015443_1_0_1; -.
DR InParanoid; Q852L0; -.
DR OMA; SSSANFW; -.
DR OrthoDB; 818507at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0106310; F:protein serine kinase activity; IEA:RHEA.
DR GO; GO:0004674; F:protein serine/threonine kinase activity; IBA:GO_Central.
DR GO; GO:0006897; P:endocytosis; IBA:GO_Central.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0009740; P:gibberellic acid mediated signaling pathway; IEA:UniProtKB-KW.
DR GO; GO:0010476; P:gibberellin mediated signaling pathway; IMP:UniProtKB.
DR GO; GO:0018105; P:peptidyl-serine phosphorylation; IBA:GO_Central.
DR GO; GO:0040008; P:regulation of growth; IEA:UniProtKB-KW.
DR GO; GO:0048586; P:regulation of long-day photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0007165; P:signal transduction; IBA:GO_Central.
DR InterPro; IPR011009; Kinase-like_dom_sf.
DR InterPro; IPR000719; Prot_kinase_dom.
DR InterPro; IPR017441; Protein_kinase_ATP_BS.
DR InterPro; IPR008271; Ser/Thr_kinase_AS.
DR Pfam; PF00069; Pkinase; 1.
DR SMART; SM00220; S_TKc; 1.
DR SUPFAM; SSF56112; SSF56112; 1.
DR PROSITE; PS00107; PROTEIN_KINASE_ATP; 1.
DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
DR PROSITE; PS00108; PROTEIN_KINASE_ST; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; Flowering; Gibberellin signaling pathway;
KW Growth regulation; Kinase; Nucleotide-binding; Nucleus; Reference proteome;
KW Serine/threonine-protein kinase; Transferase.
FT CHAIN 1..707
FT /note="Casein kinase 1-like protein HD16"
FT /id="PRO_0000437451"
FT DOMAIN 147..425
FT /note="Protein kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT REGION 19..67
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 276
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT BINDING 153..161
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT BINDING 184
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
SQ SEQUENCE 707 AA; 78811 MW; 7CB5D1EFC82E299A CRC64;
MPELRGGVWR ARLRSKKVYD VQDADPAASP VSPAPRGRTG RRGGAAAGRG NKTVAEGGGR
KALKPRGKGC RAVDLCKDQP CKDLPEVIAR KAVTGKAQED LGLNKVADRA ANLMMDGESG
DKFAAAEDES TTTPVPERVQ VGNSPEYITD RKLGKGGFGQ VYVGRRVSGG GSRTGPDAQE
VALKFEHRSS KGCNYGPPYE WQVYHTLNGC YGIPSVHYKG RLGDYYILVM DMLGPSLWDV
WNSVGQAMSA HMVACIAVEA ISILEKLHSK GFVHGDVKPE NFLLGHPGSV DEKKLFLIDL
GLASRWKEAS SGQHVDYDQR PDVFRGTIRY ASVHAHLGRT GSRRDDLESL AYTLIFLIRG
RLPWQGYQGD NKSFLVCKKK MATSPELLCC FCPAPFKHFL EMVTNMKFDE EPNYPKLISL
FDGLIEGPAS RPIRIDGALK VGQKRGRMVV NLDDDEQPKK KVRLGSPATQ WISVYNARRP
MKQRYHYNVA DSRLHQHIEK GNEDGLYISC VSSSANFWAL IMDAGTGFCS QVYELSQVFL
HKDWIMEQWE KNYYITAIAG ATNGSSLVVM SKGTPYTQQS YKVSESFPYK WINKKWKEGF
HVTSMATAGN RWGVVMSRNA GYSHQVVELD FLYPSEGIHR RWETGYRITS TAATPDQAAF
ILSIPKRKPM DETQETLRTS SFPSNHVKEK WSKNLYIASI CYGRTVC
