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P29620

- CDKD1_ORYSJ

UniProt

P29620 - CDKD1_ORYSJ

Protein

Cyclin-dependent kinase D-1

Gene

CDKD-1

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 108 (01 Oct 2014)
      Sequence version 1 (01 Apr 1993)
      Previous versions | rss
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    Functioni

    CDK-activating kinase that may control G1/S phase progression. May control the rate of cell differentiation to accomplish proper development of organs, or in response to a changing environment. Forms a complex with cyclin CYCH1-1 that phosphorylates CDKA-1 and the C-terminal domain (CTD) of the large subunit of RNA polymerase II.4 Publications

    Catalytic activityi

    ATP + a protein = ADP + a phosphoprotein.
    ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei48 – 481ATPPROSITE-ProRule annotation
    Active sitei141 – 1411Proton acceptorPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi25 – 339ATPPROSITE-ProRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. cyclin-dependent protein serine/threonine kinase activity Source: UniProtKB-EC
    3. RNA polymerase II carboxy-terminal domain kinase activity Source: UniProtKB-EC

    GO - Biological processi

    1. cell cycle Source: UniProtKB-KW
    2. cell division Source: UniProtKB-KW

    Keywords - Molecular functioni

    Kinase, Serine/threonine-protein kinase, Transferase

    Keywords - Biological processi

    Cell cycle, Cell division

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cyclin-dependent kinase D-1 (EC:2.7.11.22, EC:2.7.11.23)
    Short name:
    CDKD;1
    Alternative name(s):
    CDC2+/CDC28-related protein kinase R2
    CDK-activating kinase R2
    Short name:
    CAK-R2
    Gene namesi
    Name:CDKD-1
    Synonyms:R2
    Ordered Locus Names:Os05g0392300, LOC_Os05g32600
    ORF Names:OJ1764_D01.12
    OrganismiOryza sativa subsp. japonica (Rice)
    Taxonomic identifieri39947 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
    ProteomesiUP000000763: Chromosome 5

    Organism-specific databases

    GrameneiP29620.

    Subcellular locationi

    Nucleus 1 Publication

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 424424Cyclin-dependent kinase D-1PRO_0000086074Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei29 – 291PhosphothreonineBy similarity
    Modified residuei30 – 301PhosphotyrosineBy similarity
    Modified residuei168 – 1681PhosphoserineBy similarity
    Modified residuei174 – 1741PhosphothreonineBy similarity

    Keywords - PTMi

    Phosphoprotein

    Expressioni

    Tissue specificityi

    Expressed in actively dividing cells of roots, leaves and shoots. Expressed in the intercalary meristem and the elongation zone of internodes.4 Publications

    Developmental stagei

    Expression reaches a peak in the G1/S phases and then decreases in the G2/M phases.2 Publications

    Inductioni

    By gibberellic acid (GA3) and submergence in the meristematic zone of internodes. Down-regulated by auxin.4 Publications

    Interactioni

    Subunit structurei

    Interacts with CYCH1-1.1 Publication

    Structurei

    3D structure databases

    ProteinModelPortaliP29620.
    SMRiP29620. Positions 21-314.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini19 – 299281Protein kinasePROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 protein kinase domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0515.
    KOiK02202.
    OMAiCHRNWIL.

    Family and domain databases

    InterProiIPR011009. Kinase-like_dom.
    IPR000719. Prot_kinase_dom.
    IPR017441. Protein_kinase_ATP_BS.
    IPR002290. Ser/Thr_dual-sp_kinase_dom.
    IPR008271. Ser/Thr_kinase_AS.
    [Graphical view]
    PfamiPF00069. Pkinase. 1 hit.
    [Graphical view]
    SMARTiSM00220. S_TKc. 1 hit.
    [Graphical view]
    SUPFAMiSSF56112. SSF56112. 1 hit.
    PROSITEiPS00107. PROTEIN_KINASE_ATP. 1 hit.
    PS50011. PROTEIN_KINASE_DOM. 1 hit.
    PS00108. PROTEIN_KINASE_ST. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P29620-1 [UniParc]FASTAAdd to Basket

    « Hide

    MASGDGGDDA GVKRVADRYL KREVLGEGTY GVVFKAVDTK TGNTVAIKKI    50
    RLGKYKEGVN FTALREIKLL KELKDSNIIE LIDAFPYKGN LHLVFEFMET 100
    DLEAVIRDRN IVLSPADTKS YIQMMLKGLA FCHKKWVLHR DMKPNNLLIG 150
    ADGQLKLADF GLARIFGSPE RNFTHQVFAR WYRAPELLFG TKQYGSAVDI 200
    WAAGCIFAEL LLRRPFLQGS SDIDQLGKIF AAFGTPKSSQ WPDMVYLPDY 250
    VEYQFVSAPP LRSLFPMASD DALDLLSRMF TYDPKARITA QQALEHRYFL 300
    SVPAPTKPSQ LPRPPPKGDS GNNKIPDLNL QDGPVVLSPP RKLRRVTAHE 350
    GMEVHMHRAD RTEEHPSGAR HMDDMSSQSS RIPMSVDVGA IFGTRPAPRP 400
    TLNSADKSRL KRKLDMDPEF GYTE 424
    Length:424
    Mass (Da):47,613
    Last modified:April 1, 1993 - v1
    Checksum:i28606BE7120BB048
    GO

    Sequence cautioni

    The sequence AAV31263.1 differs from that shown. Reason: Erroneous gene model prediction.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X58194 mRNA. Translation: CAA41172.1.
    AC107085 Genomic DNA. Translation: AAV31263.1. Sequence problems.
    AP008211 Genomic DNA. Translation: BAF17364.1.
    PIRiS13934.
    RefSeqiNP_001055450.1. NM_001061985.1.
    UniGeneiOs.2689.

    Genome annotation databases

    GeneIDi4338689.
    KEGGiosa:4338689.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X58194 mRNA. Translation: CAA41172.1 .
    AC107085 Genomic DNA. Translation: AAV31263.1 . Sequence problems.
    AP008211 Genomic DNA. Translation: BAF17364.1 .
    PIRi S13934.
    RefSeqi NP_001055450.1. NM_001061985.1.
    UniGenei Os.2689.

    3D structure databases

    ProteinModelPortali P29620.
    SMRi P29620. Positions 21-314.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 4338689.
    KEGGi osa:4338689.

    Organism-specific databases

    Gramenei P29620.

    Phylogenomic databases

    eggNOGi COG0515.
    KOi K02202.
    OMAi CHRNWIL.

    Family and domain databases

    InterProi IPR011009. Kinase-like_dom.
    IPR000719. Prot_kinase_dom.
    IPR017441. Protein_kinase_ATP_BS.
    IPR002290. Ser/Thr_dual-sp_kinase_dom.
    IPR008271. Ser/Thr_kinase_AS.
    [Graphical view ]
    Pfami PF00069. Pkinase. 1 hit.
    [Graphical view ]
    SMARTi SM00220. S_TKc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56112. SSF56112. 1 hit.
    PROSITEi PS00107. PROTEIN_KINASE_ATP. 1 hit.
    PS50011. PROTEIN_KINASE_DOM. 1 hit.
    PS00108. PROTEIN_KINASE_ST. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "cDNA cloning of a novel cdc2+/CDC28-related protein kinase from rice."
      Hata S.
      FEBS Lett. 279:149-152(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: cv. Nipponbare.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Nipponbare.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Nipponbare.
    4. "The rice annotation project database (RAP-DB): 2008 update."
      The rice annotation project (RAP)
      Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENOME REANNOTATION.
      Strain: cv. Nipponbare.
    5. "Differential expression of a CAK (cdc2-activating kinase)-like protein kinase, cyclins and cdc2 genes from rice during the cell cycle and in response to gibberellin."
      Sauter M.
      Plant J. 11:181-190(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INDUCTION.
    6. "A rice homolog of Cdk7/MO15 phosphorylates both cyclin-dependent protein kinases and the carboxy-terminal domain of RNA polymerase II."
      Yamaguchi M., Umeda M., Uchimiya H.
      Plant J. 16:613-619(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    7. "Adventitious root growth and cell-cycle induction in deepwater rice."
      Lorbiecke R., Sauter M.
      Plant Physiol. 119:21-30(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    8. "Differential expression of genes for cyclin-dependent protein kinases in rice plants."
      Umeda M., Umeda-Hara C., Yamaguchi M., Hashimoto J., Uchimiya H.
      Plant Physiol. 119:31-40(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY.
    9. "Activation of CDK-activating kinase is dependent on interaction with H-type cyclins in plants."
      Yamaguchi M., Fabian T., Sauter M., Bhalerao R.P., Schrader J., Sandberg G., Umeda M., Uchimiya H.
      Plant J. 24:11-20(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY, INTERACTION WITH CYCH1-1.
    10. "The rice cyclin-dependent kinase-activating kinase R2 regulates S-phase progression."
      Fabian-Marwedel T., Umeda M., Sauter M.
      Plant Cell 14:197-210(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INDUCTION.
    11. "Control of in vitro organogenesis by cyclin-dependent kinase activities in plants."
      Yamaguchi M., Kato H., Yoshida S., Yamamura S., Uchimiya H., Umeda M.
      Proc. Natl. Acad. Sci. U.S.A. 100:8019-8023(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    12. "Genome-wide identification and expression analysis of rice cell cycle genes."
      Guo J., Song J., Wang F., Zhang X.S.
      Plant Mol. Biol. 64:349-360(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION AND GENE FAMILY.

    Entry informationi

    Entry nameiCDKD1_ORYSJ
    AccessioniPrimary (citable) accession number: P29620
    Secondary accession number(s): Q0DIF9, Q60ES0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1993
    Last sequence update: April 1, 1993
    Last modified: October 1, 2014
    This is version 108 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Oryza sativa (rice)
      Index of Oryza sativa entries and their corresponding gene designations
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3