CDKD1_ORYSJ
ID CDKD1_ORYSJ Reviewed; 424 AA.
AC P29620; Q0DIF9; Q60ES0;
DT 01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1993, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=Cyclin-dependent kinase D-1;
DE Short=CDKD;1;
DE EC=2.7.11.22;
DE EC=2.7.11.23;
DE AltName: Full=CDC2+/CDC28-related protein kinase R2;
DE AltName: Full=CDK-activating kinase R2;
DE Short=CAK-R2;
GN Name=CDKD-1; Synonyms=R2; OrderedLocusNames=Os05g0392300, LOC_Os05g32600;
GN ORFNames=OJ1764_D01.12;
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].
RC STRAIN=cv. Nipponbare;
RX PubMed=1995335; DOI=10.1016/0014-5793(91)80271-4;
RA Hata S.;
RT "cDNA cloning of a novel cdc2+/CDC28-related protein kinase from rice.";
RL FEBS Lett. 279:149-152(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16261349; DOI=10.1007/s00438-005-0039-y;
RA Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J.,
RA Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F.,
RA Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y.;
RT "A fine physical map of the rice chromosome 5.";
RL Mol. Genet. Genomics 274:337-345(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 TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND INDUCTION.
RX PubMed=9076986; DOI=10.1046/j.1365-313x.1997.11020181.x;
RA Sauter M.;
RT "Differential expression of a CAK (cdc2-activating kinase)-like protein
RT kinase, cyclins and cdc2 genes from rice during the cell cycle and in
RT response to gibberellin.";
RL Plant J. 11:181-190(1997).
RN [7]
RP FUNCTION.
RX PubMed=10036778; DOI=10.1046/j.1365-313x.1998.00338.x;
RA Yamaguchi M., Umeda M., Uchimiya H.;
RT "A rice homolog of Cdk7/MO15 phosphorylates both cyclin-dependent protein
RT kinases and the carboxy-terminal domain of RNA polymerase II.";
RL Plant J. 16:613-619(1998).
RN [8]
RP INDUCTION.
RX PubMed=9880342; DOI=10.1104/pp.119.1.21;
RA Lorbiecke R., Sauter M.;
RT "Adventitious root growth and cell-cycle induction in deepwater rice.";
RL Plant Physiol. 119:21-30(1999).
RN [9]
RP TISSUE SPECIFICITY.
RX PubMed=9880343; DOI=10.1104/pp.119.1.31;
RA Umeda M., Umeda-Hara C., Yamaguchi M., Hashimoto J., Uchimiya H.;
RT "Differential expression of genes for cyclin-dependent protein kinases in
RT rice plants.";
RL Plant Physiol. 119:31-40(1999).
RN [10]
RP FUNCTION, TISSUE SPECIFICITY, AND INTERACTION WITH CYCH1-1.
RX PubMed=11029700; DOI=10.1046/j.1365-313x.2000.00846.x;
RA Yamaguchi M., Fabian T., Sauter M., Bhalerao R.P., Schrader J.,
RA Sandberg G., Umeda M., Uchimiya H.;
RT "Activation of CDK-activating kinase is dependent on interaction with H-
RT type cyclins in plants.";
RL Plant J. 24:11-20(2000).
RN [11]
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE,
RP AND INDUCTION.
RX PubMed=11826308; DOI=10.1105/tpc.010386;
RA Fabian-Marwedel T., Umeda M., Sauter M.;
RT "The rice cyclin-dependent kinase-activating kinase R2 regulates S-phase
RT progression.";
RL Plant Cell 14:197-210(2002).
RN [12]
RP FUNCTION.
RX PubMed=12799469; DOI=10.1073/pnas.1332637100;
RA Yamaguchi M., Kato H., Yoshida S., Yamamura S., Uchimiya H., Umeda M.;
RT "Control of in vitro organogenesis by cyclin-dependent kinase activities in
RT plants.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:8019-8023(2003).
RN [13]
RP INDUCTION AND GENE FAMILY.
RX PubMed=17443292; DOI=10.1007/s11103-007-9154-y;
RA Guo J., Song J., Wang F., Zhang X.S.;
RT "Genome-wide identification and expression analysis of rice cell cycle
RT genes.";
RL Plant Mol. Biol. 64:349-360(2007).
CC -!- FUNCTION: CDK-activating kinase that may control G1/S phase
CC progression. May control the rate of cell differentiation to accomplish
CC proper development of organs, or in response to a changing environment.
CC Forms a complex with cyclin CYCH1-1 that phosphorylates CDKA-1 and the
CC C-terminal domain (CTD) of the large subunit of RNA polymerase II.
CC {ECO:0000269|PubMed:10036778, ECO:0000269|PubMed:11029700,
CC ECO:0000269|PubMed:11826308, ECO:0000269|PubMed:12799469}.
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=2.7.11.22;
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=2.7.11.22;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[DNA-directed RNA polymerase] + ATP = ADP + H(+) + phospho-
CC [DNA-directed RNA polymerase]; Xref=Rhea:RHEA:10216, Rhea:RHEA-
CC COMP:11321, Rhea:RHEA-COMP:11322, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:43176, ChEBI:CHEBI:68546,
CC ChEBI:CHEBI:456216; EC=2.7.11.23;
CC -!- SUBUNIT: Interacts with CYCH1-1. {ECO:0000269|PubMed:11029700}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11826308}.
CC -!- TISSUE SPECIFICITY: Expressed in actively dividing cells of roots,
CC leaves and shoots. Expressed in the intercalary meristem and the
CC elongation zone of internodes. {ECO:0000269|PubMed:11029700,
CC ECO:0000269|PubMed:11826308, ECO:0000269|PubMed:9076986,
CC ECO:0000269|PubMed:9880343}.
CC -!- DEVELOPMENTAL STAGE: Expression reaches a peak in the G1/S phases and
CC then decreases in the G2/M phases. {ECO:0000269|PubMed:11826308,
CC ECO:0000269|PubMed:9076986}.
CC -!- INDUCTION: By gibberellic acid (GA3) and submergence in the
CC meristematic zone of internodes. Down-regulated by auxin.
CC {ECO:0000269|PubMed:11826308, ECO:0000269|PubMed:17443292,
CC ECO:0000269|PubMed:9076986, ECO:0000269|PubMed:9880342}.
CC -!- SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr
CC protein kinase family. CDC2/CDKX subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAV31263.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; X58194; CAA41172.1; -; mRNA.
DR EMBL; AC107085; AAV31263.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008211; BAF17364.1; -; Genomic_DNA.
DR EMBL; AP014961; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; S13934; S13934.
DR RefSeq; XP_015640677.1; XM_015785191.1.
DR AlphaFoldDB; P29620; -.
DR SMR; P29620; -.
DR STRING; 4530.OS05T0392300-01; -.
DR PaxDb; P29620; -.
DR PRIDE; P29620; -.
DR GeneID; 4338689; -.
DR KEGG; osa:4338689; -.
DR eggNOG; KOG0659; Eukaryota.
DR HOGENOM; CLU_114282_0_0_1; -.
DR InParanoid; P29620; -.
DR OrthoDB; 1367115at2759; -.
DR PlantReactome; R-OSA-9640760; G1 phase.
DR Proteomes; UP000000763; Chromosome 5.
DR Proteomes; UP000059680; Chromosome 5.
DR Genevisible; P29620; OS.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0070985; C:transcription factor TFIIK complex; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004693; F:cyclin-dependent protein serine/threonine kinase activity; IBA:GO_Central.
DR GO; GO:0106310; F:protein serine kinase activity; IEA:RHEA.
DR GO; GO:0008353; F:RNA polymerase II CTD heptapeptide repeat kinase activity; IBA:GO_Central.
DR GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0006468; P:protein phosphorylation; IBA:GO_Central.
DR CDD; cd07841; STKc_CDK7; 1.
DR InterPro; IPR037770; CDK7.
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; Cell cycle; Cell division; Kinase; Nucleotide-binding;
KW Nucleus; Phosphoprotein; Reference proteome;
KW Serine/threonine-protein kinase; Transferase.
FT CHAIN 1..424
FT /note="Cyclin-dependent kinase D-1"
FT /id="PRO_0000086074"
FT DOMAIN 19..299
FT /note="Protein kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT REGION 303..337
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 359..424
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 405..424
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 141
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159,
FT ECO:0000255|PROSITE-ProRule:PRU10027"
FT BINDING 25..33
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT BINDING 48
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT MOD_RES 29
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250"
FT MOD_RES 30
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000250"
FT MOD_RES 168
FT /note="Phosphoserine"
FT /evidence="ECO:0000250"
FT MOD_RES 174
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250"
SQ SEQUENCE 424 AA; 47613 MW; 28606BE7120BB048 CRC64;
MASGDGGDDA GVKRVADRYL KREVLGEGTY GVVFKAVDTK TGNTVAIKKI RLGKYKEGVN
FTALREIKLL KELKDSNIIE LIDAFPYKGN LHLVFEFMET DLEAVIRDRN IVLSPADTKS
YIQMMLKGLA FCHKKWVLHR DMKPNNLLIG ADGQLKLADF GLARIFGSPE RNFTHQVFAR
WYRAPELLFG TKQYGSAVDI WAAGCIFAEL LLRRPFLQGS SDIDQLGKIF AAFGTPKSSQ
WPDMVYLPDY VEYQFVSAPP LRSLFPMASD DALDLLSRMF TYDPKARITA QQALEHRYFL
SVPAPTKPSQ LPRPPPKGDS GNNKIPDLNL QDGPVVLSPP RKLRRVTAHE GMEVHMHRAD
RTEEHPSGAR HMDDMSSQSS RIPMSVDVGA IFGTRPAPRP TLNSADKSRL KRKLDMDPEF
GYTE
