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Q9C9M7

- CDKD2_ARATH

UniProt

Q9C9M7 - CDKD2_ARATH

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Protein

Cyclin-dependent kinase D-2

Gene

CDKD-2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Forms a stable complex with cyclin CYCH1-1 that phosphorylates human CDK2 and the C-terminal domain (CTD) of the large subunit of RNA polymerase II.2 Publications

Catalytic activityi

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

Enzyme regulationi

Activated by phosphorylation by CDKF-1. Down-regulated by phosphorylation by WEE1.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei42 – 421ATPCurated
Active sitei135 – 1351Proton acceptorPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi19 – 279ATPPROSITE-ProRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. cyclin-dependent protein serine/threonine kinase activity Source: UniProtKB-EC
  3. protein serine/threonine kinase activity Source: TAIR
  4. 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
  3. regulation of cyclin-dependent protein serine/threonine kinase activity Source: TAIR
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

Enzyme and pathway databases

BioCyciARA:AT1G66750-MONOMER.
ReactomeiREACT_230366. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
REACT_231323. Dual incision reaction in TC-NER.
REACT_244453. RNA Polymerase II Transcription Initiation And Promoter Clearance.
REACT_247918. Dual incision reaction in GG-NER.
REACT_251417. Formation of incision complex in GG-NER.
REACT_251761. RNA Polymerase II Promoter Escape.
REACT_257408. RNA Polymerase II Transcription Initiation.
REACT_259973. RNA Polymerase II Pre-transcription Events.
REACT_260138. mRNA Capping.
REACT_260665. Formation of the Early Elongation Complex.
REACT_261061. Formation of transcription-coupled NER (TC-NER) repair complex.
REACT_261268. RNA Pol II CTD phosphorylation and interaction with CE.

Names & Taxonomyi

Protein namesi
Recommended name:
Cyclin-dependent kinase D-2 (EC:2.7.11.22, EC:2.7.11.23)
Short name:
CDKD;2
Alternative name(s):
CDK-activating kinase 4-At
Short name:
CAK4-At
Gene namesi
Name:CDKD-2
Ordered Locus Names:At1g66750
ORF Names:F4N21.12
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 1

Organism-specific databases

TAIRiAT1G66750.

Subcellular locationi

Cytoplasm 1 Publication. Nucleus 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: TAIR
  2. nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi24 – 241Y → F: Abolishes phosphorylation by WEE1. 1 Publication
Mutagenesisi42 – 421K → R: Prevents autophosphorylation. 1 Publication
Mutagenesisi162 – 1621S → A: Reduces phosphorylation by CDKF-1 by 30%. 1 Publication
Mutagenesisi168 – 1681T → A: Almost abolishes phosphorylation by CDKF-1. Loss of CTD-kinase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 348348Cyclin-dependent kinase D-2PRO_0000293120Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei24 – 241Phosphotyrosine1 Publication
Modified residuei162 – 1621Phosphoserine; by CAK1 Publication
Modified residuei168 – 1681Phosphothreonine; by CAK1 Publication

Post-translational modificationi

Phosphorylated by CDKF-1 at Ser-162 and Thr-168. Phosphorylated by WEE1 at Tyr-24. Autophosphorylated.2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9C9M7.
PRIDEiQ9C9M7.

Expressioni

Tissue specificityi

Expressed in suspension cell culture, but not in plant organs.1 Publication

Gene expression databases

GenevestigatoriQ9C9M7.

Interactioni

Subunit structurei

Interacts with CYCH1-1. Binding to CYCH1-1 activates CDK kinase.2 Publications

Protein-protein interaction databases

BioGridi28214. 43 interactions.
IntActiQ9C9M7. 22 interactions.
STRINGi3702.AT1G66750.1-P.

Structurei

3D structure databases

ProteinModelPortaliQ9C9M7.
SMRiQ9C9M7. Positions 16-310.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini13 – 293281Protein kinasePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 protein kinase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0515.
HOGENOMiHOG000233024.
InParanoidiQ9C9M7.
KOiK02202.
OMAiPNRINTH.
PhylomeDBiQ9C9M7.

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.

Q9C9M7-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSKSGDNQPV DRYLRRQILG EGTYGVVYKA TDTKTGKTVA VKKIRLGNQK
60 70 80 90 100
EGVNFTALRE IKLLKELNHP HIVELIDAFP HDGSLHLVFE YMQTDLEAVI
110 120 130 140 150
RDRNIFLSPG DIKSYMLMTL KGLAYCHKKW VLHRDMKPNN LLIGENGLLK
160 170 180 190 200
LADFGLARLF GSPNRRFTHQ VFATWYRAPE LLFGSRQYGA GVDVWAAGCI
210 220 230 240 250
FAELLLRRPF LPGSTEIDQL GKIFQAFGTP VPSQWSDMIY LPDYMEFSYT
260 270 280 290 300
PAPPLRTIFP MASDDALDLL AKMFIYDPRQ RITIQQALDH RYFSSSPSPT
310 320 330 340
EPGKLQIPAS KGDALEPKAS EQNQHGNSPA VLSPPGKMRR VMGPEGFT
Length:348
Mass (Da):39,201
Last modified:June 1, 2001 - v1
Checksum:iA32CA3E98204DDAD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB074116 mRNA. Translation: BAB91558.1.
AC013288 Genomic DNA. Translation: AAG60076.1.
CP002684 Genomic DNA. Translation: AEE34551.1.
AY136355 mRNA. Translation: AAM97021.1.
BT000198 mRNA. Translation: AAN15517.1.
RefSeqiNP_176847.1. NM_105345.4.
UniGeneiAt.35737.

Genome annotation databases

EnsemblPlantsiAT1G66750.1; AT1G66750.1; AT1G66750.
GeneIDi842993.
KEGGiath:AT1G66750.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB074116 mRNA. Translation: BAB91558.1 .
AC013288 Genomic DNA. Translation: AAG60076.1 .
CP002684 Genomic DNA. Translation: AEE34551.1 .
AY136355 mRNA. Translation: AAM97021.1 .
BT000198 mRNA. Translation: AAN15517.1 .
RefSeqi NP_176847.1. NM_105345.4.
UniGenei At.35737.

3D structure databases

ProteinModelPortali Q9C9M7.
SMRi Q9C9M7. Positions 16-310.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 28214. 43 interactions.
IntActi Q9C9M7. 22 interactions.
STRINGi 3702.AT1G66750.1-P.

Proteomic databases

PaxDbi Q9C9M7.
PRIDEi Q9C9M7.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT1G66750.1 ; AT1G66750.1 ; AT1G66750 .
GeneIDi 842993.
KEGGi ath:AT1G66750.

Organism-specific databases

GeneFarmi 3289. 109.
TAIRi AT1G66750.

Phylogenomic databases

eggNOGi COG0515.
HOGENOMi HOG000233024.
InParanoidi Q9C9M7.
KOi K02202.
OMAi PNRINTH.
PhylomeDBi Q9C9M7.

Enzyme and pathway databases

BioCyci ARA:AT1G66750-MONOMER.
Reactomei REACT_230366. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
REACT_231323. Dual incision reaction in TC-NER.
REACT_244453. RNA Polymerase II Transcription Initiation And Promoter Clearance.
REACT_247918. Dual incision reaction in GG-NER.
REACT_251417. Formation of incision complex in GG-NER.
REACT_251761. RNA Polymerase II Promoter Escape.
REACT_257408. RNA Polymerase II Transcription Initiation.
REACT_259973. RNA Polymerase II Pre-transcription Events.
REACT_260138. mRNA Capping.
REACT_260665. Formation of the Early Elongation Complex.
REACT_261061. Formation of transcription-coupled NER (TC-NER) repair complex.
REACT_261268. RNA Pol II CTD phosphorylation and interaction with CE.

Gene expression databases

Genevestigatori Q9C9M7.

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. "Differential phosphorylation activities of CDK-activating kinases in Arabidopsis thaliana."
    Shimotohno A., Matsubayashi S., Yamaguchi M., Uchimiya H., Umeda M.
    FEBS Lett. 534:69-74(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
  2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Genome-wide analysis of core cell cycle genes in Arabidopsis."
    Vandepoele K., Raes J., de Veylder L., Rouze P., Rombauts S., Inze D.
    Plant Cell 14:903-916(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE.
  6. "The plant-specific kinase CDKF;1 is involved in activating phosphorylation of cyclin-dependent kinase-activating kinases in Arabidopsis."
    Shimotohno A., Umeda-Hara C., Bisova K., Uchimiya H., Umeda M.
    Plant Cell 16:2954-2966(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION, SUBCELLULAR LOCATION, INTERACTION WITH CYCH1-1, PHOSPHORYLATION AT SER-162 AND THR-168, MUTAGENESIS OF LYS-42; SER-162 AND THR-168.
  7. "Cell cycle regulation in plant development."
    Inze D., de Veylder L.
    Annu. Rev. Genet. 40:77-105(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  8. "Diverse phosphoregulatory mechanisms controlling cyclin-dependent kinase-activating kinases in Arabidopsis."
    Shimotohno A., Ohno R., Bisova K., Sakaguchi N., Huang J., Koncz C., Uchimiya H., Umeda M.
    Plant J. 47:701-710(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION, PHOSPHORYLATION AT TYR-24, INTERACTION WITH CYCH1-1, MUTAGENESIS OF TYR-24.

Entry informationi

Entry nameiCDKD2_ARATH
AccessioniPrimary (citable) accession number: Q9C9M7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 10, 2007
Last sequence update: June 1, 2001
Last modified: November 26, 2014
This is version 102 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. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3