CDKD3_ARATH
ID CDKD3_ARATH Reviewed; 391 AA.
AC Q9LMT0; Q9LM42;
DT 10-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=Cyclin-dependent kinase D-3;
DE Short=CDKD;3;
DE EC=2.7.11.22;
DE EC=2.7.11.23;
DE AltName: Full=CDK-activating kinase 2-At;
DE Short=CAK2-At;
GN Name=CDKD-3; OrderedLocusNames=At1g18040; ORFNames=T10F20.5, T10O22.1;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND TISSUE SPECIFICITY.
RX PubMed=12527363; DOI=10.1016/s0014-5793(02)03780-8;
RA Shimotohno A., Matsubayashi S., Yamaguchi M., Uchimiya H., Umeda M.;
RT "Differential phosphorylation activities of CDK-activating kinases in
RT Arabidopsis thaliana.";
RL FEBS Lett. 534:69-74(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=11971144; DOI=10.1105/tpc.010445;
RA Vandepoele K., Raes J., de Veylder L., Rouze P., Rombauts S., Inze D.;
RT "Genome-wide analysis of core cell cycle genes in Arabidopsis.";
RL Plant Cell 14:903-916(2002).
RN [6]
RP FUNCTION, ACTIVITY REGULATION, SUBCELLULAR LOCATION, INTERACTION WITH
RP CYCH1-1, PHOSPHORYLATION AT SER-161 AND THR-167, AND MUTAGENESIS OF LYS-41;
RP SER-161 AND THR-167.
RX PubMed=15486101; DOI=10.1105/tpc.104.025601;
RA Shimotohno A., Umeda-Hara C., Bisova K., Uchimiya H., Umeda M.;
RT "The plant-specific kinase CDKF;1 is involved in activating phosphorylation
RT of cyclin-dependent kinase-activating kinases in Arabidopsis.";
RL Plant Cell 16:2954-2966(2004).
RN [7]
RP REVIEW.
RX PubMed=17094738; DOI=10.1146/annurev.genet.40.110405.090431;
RA Inze D., de Veylder L.;
RT "Cell cycle regulation in plant development.";
RL Annu. Rev. Genet. 40:77-105(2006).
RN [8]
RP FUNCTION, PHOSPHORYLATION AT TYR-23, INTERACTION WITH CYCH1-1, AND
RP MUTAGENESIS OF TYR-23.
RX PubMed=16856985; DOI=10.1111/j.1365-313x.2006.02820.x;
RA Shimotohno A., Ohno R., Bisova K., Sakaguchi N., Huang J., Koncz C.,
RA Uchimiya H., Umeda M.;
RT "Diverse phosphoregulatory mechanisms controlling cyclin-dependent kinase-
RT activating kinases in Arabidopsis.";
RL Plant J. 47:701-710(2006).
CC -!- FUNCTION: May form a stable complex with cyclin CYCH1-1 that
CC phosphorylates human CDK2 and the C-terminal domain (CTD) of the large
CC subunit of RNA polymerase II. {ECO:0000269|PubMed:15486101,
CC ECO:0000269|PubMed:16856985}.
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 -!- ACTIVITY REGULATION: Activated by phosphorylation by CDKF-1.
CC {ECO:0000269|PubMed:15486101}.
CC -!- SUBUNIT: Interacts with CYCH1-1. Binding to CYCH1-1 activates CDK
CC kinase. {ECO:0000269|PubMed:15486101, ECO:0000269|PubMed:16856985}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15486101}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, shoots and suspension cell
CC culture. {ECO:0000269|PubMed:12527363}.
CC -!- PTM: Phosphorylated by CDKF-1 at Ser-161 and Thr-167. Phosphorylated at
CC Tyr-23 by WEE1. Autophosphorylated. {ECO:0000269|PubMed:15486101,
CC ECO:0000269|PubMed:16856985}.
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=AAF78394.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB047274; BAB62843.1; -; mRNA.
DR EMBL; AC034107; AAF97821.1; -; Genomic_DNA.
DR EMBL; AC069551; AAF78394.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE29667.1; -; Genomic_DNA.
DR EMBL; AY099677; AAM20528.1; -; mRNA.
DR EMBL; AY128857; AAM91257.1; -; mRNA.
DR PIR; H86315; H86315.
DR RefSeq; NP_173244.1; NM_101666.3.
DR AlphaFoldDB; Q9LMT0; -.
DR SMR; Q9LMT0; -.
DR BioGRID; 23623; 33.
DR IntAct; Q9LMT0; 6.
DR STRING; 3702.AT1G18040.1; -.
DR iPTMnet; Q9LMT0; -.
DR PaxDb; Q9LMT0; -.
DR PRIDE; Q9LMT0; -.
DR ProteomicsDB; 224472; -.
DR EnsemblPlants; AT1G18040.1; AT1G18040.1; AT1G18040.
DR GeneID; 838384; -.
DR Gramene; AT1G18040.1; AT1G18040.1; AT1G18040.
DR KEGG; ath:AT1G18040; -.
DR Araport; AT1G18040; -.
DR TAIR; locus:2194045; AT1G18040.
DR eggNOG; KOG0659; Eukaryota.
DR HOGENOM; CLU_000288_181_0_1; -.
DR InParanoid; Q9LMT0; -.
DR OMA; TQSYLRM; -.
DR OrthoDB; 1367115at2759; -.
DR PhylomeDB; Q9LMT0; -.
DR PRO; PR:Q9LMT0; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9LMT0; baseline and differential.
DR Genevisible; Q9LMT0; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
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:0004672; F:protein kinase activity; TAS:TAIR.
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 GO; GO:0051726; P:regulation of cell cycle; TAS:TAIR.
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..391
FT /note="Cyclin-dependent kinase D-3"
FT /id="PRO_0000293121"
FT DOMAIN 12..292
FT /note="Protein kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT REGION 294..321
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 337..391
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 377..391
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 134
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159,
FT ECO:0000255|PROSITE-ProRule:PRU10027"
FT BINDING 18..26
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT BINDING 41
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305"
FT MOD_RES 23
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000269|PubMed:16856985"
FT MOD_RES 161
FT /note="Phosphoserine; by CAK"
FT /evidence="ECO:0000269|PubMed:15486101"
FT MOD_RES 167
FT /note="Phosphothreonine; by CAK"
FT /evidence="ECO:0000269|PubMed:15486101"
FT MUTAGEN 23
FT /note="Y->F: Abolishes phosphorylation by WEE1."
FT /evidence="ECO:0000269|PubMed:16856985"
FT MUTAGEN 41
FT /note="K->R: Prevents autophosphorylation."
FT /evidence="ECO:0000269|PubMed:15486101"
FT MUTAGEN 161
FT /note="S->A: Reduces phosphorylation by CDKF-1 by 20%.
FT Abolishes phosphorylation by CDKF-1; when associated with
FT A-167."
FT /evidence="ECO:0000269|PubMed:15486101"
FT MUTAGEN 167
FT /note="T->A: Reduces phosphorylation by CDKF-1 by 80%.
FT Abolishes phosphorylation by CDKF-1; when associated with
FT A-161."
FT /evidence="ECO:0000269|PubMed:15486101"
SQ SEQUENCE 391 AA; 44530 MW; 3FD4A2293283B656 CRC64;
MPEQPKKVAD RYLKQEVLGQ GTYGVVFKAT DTKTEQTVAI KKIRLGKQRE GVNITALREI
KMLKELKHPH IILLIDAFPH KENLHLVFEF METDLEAVIR DSNIFLSPAD IKSYLLMTFK
GLAYCHDKWV LHRDMKPNNL LIGVDGQLKL ADFGLARIFG SPNRKFTHQV FARWYRAPEL
LFGAKQYGAA VDVWAVACIF AELLLRRPFL QGNSDIDQLS KIFAAFGTPK ADQWPDLTKL
PDYVEYQFVP APSLRSLFPA VSDDALDLLS KMFTYDPKAR ISIKQALEHR YFTSAPAPTD
PAKLPKPVPK QDGKSSYGKH EAITVQSPPR KLRRVMPERG RVDSLKSHVD KDQQAPMSLD
FTILAERPPN RPTITSADRS HLKRKLDLEF Q
