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P29620

- CDKD1_ORYSJ

UniProt

P29620 - CDKD1_ORYSJ

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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

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
Complete GO annotation...

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-KW
Complete GO annotation...

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

Gene expression databases

ExpressionAtlasiP29620. baseline.

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.
InParanoidiP29620.
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.
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

        10         20         30         40         50
MASGDGGDDA GVKRVADRYL KREVLGEGTY GVVFKAVDTK TGNTVAIKKI
60 70 80 90 100
RLGKYKEGVN FTALREIKLL KELKDSNIIE LIDAFPYKGN LHLVFEFMET
110 120 130 140 150
DLEAVIRDRN IVLSPADTKS YIQMMLKGLA FCHKKWVLHR DMKPNNLLIG
160 170 180 190 200
ADGQLKLADF GLARIFGSPE RNFTHQVFAR WYRAPELLFG TKQYGSAVDI
210 220 230 240 250
WAAGCIFAEL LLRRPFLQGS SDIDQLGKIF AAFGTPKSSQ WPDMVYLPDY
260 270 280 290 300
VEYQFVSAPP LRSLFPMASD DALDLLSRMF TYDPKARITA QQALEHRYFL
310 320 330 340 350
SVPAPTKPSQ LPRPPPKGDS GNNKIPDLNL QDGPVVLSPP RKLRRVTAHE
360 370 380 390 400
GMEVHMHRAD RTEEHPSGAR HMDDMSSQSS RIPMSVDVGA IFGTRPAPRP
410 420
TLNSADKSRL KRKLDMDPEF GYTE
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. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.
InParanoidi P29620.
KOi K02202.
OMAi CHRNWIL.

Gene expression databases

ExpressionAtlasi P29620. baseline.

Family and domain databases

InterProi IPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR002290. Ser/Thr_dual-sp_kinase.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 109 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