Cyclin-dependent kinase D-1 - Oryza sativa subsp. japonica (Rice)

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P29620 (CDKD1_ORYSJ) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 101. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Cyclin-dependent kinase D-1
Short name=CDKD;1
EC=2.7.11.22
EC=2.7.11.23

Alternative name(s):
CDC2+/CDC28-related protein kinase R2
CDK-activating kinase R2
Short name=CAK-R2

Gene names

Name:	CDKD-1
Synonyms:	R2
Ordered Locus Names:	Os05g0392300, LOC_Os05g32600
ORF Names:	OJ1764_D01.12

Organism

Oryza sativa subsp. japonica (Rice) [Reference proteome]

Taxonomic identifier

39947 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › BEP clade › Ehrhartoideae › Oryzeae › Oryza ›

Protein attributes

Sequence length	424 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.6 Ref.9 Ref.10 Ref.11
Catalytic activity	ATP + a protein = ADP + a phosphoprotein. ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate.
Subunit structure	Interacts with CYCH1-1. Ref.9
Subcellular location	Nucleus Ref.10.
Tissue specificity	Expressed in actively dividing cells of roots, leaves and shoots. Expressed in the intercalary meristem and the elongation zone of internodes. Ref.5 Ref.8 Ref.9 Ref.10
Developmental stage	Expression reaches a peak in the G1/S phases and then decreases in the G2/M phases. Ref.5 Ref.10
Induction	By gibberellic acid (GA3) and submergence in the meristematic zone of internodes. Down-regulated by auxin. Ref.5 Ref.7 Ref.10 Ref.12
Sequence similarities	Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily. Contains 1 protein kinase domain.
Sequence caution	The sequence AAV31263.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Cell cycle Cell division
Cellular component	Nucleus
Ligand	ATP-binding Nucleotide-binding
Molecular function	Kinase Serine/threonine-protein kinase Transferase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell division Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: EnsemblPlants/Gramene nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA polymerase II carboxy-terminal domain kinase activity Inferred from electronic annotation. Source: EC cyclin-dependent protein serine/threonine kinase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 424

424

Cyclin-dependent kinase D-1

PRO_0000086074

Regions

Domain

19 – 299

281

Protein kinase

Nucleotide binding

25 – 33

ATP By similarity

Sites

Active site

141

Proton acceptor By similarity

Binding site

ATP By similarity

Amino acid modifications

Modified residue

Phosphothreonine By similarity

Modified residue

Phosphotyrosine By similarity

Modified residue

168

Phosphoserine By similarity

Modified residue

174

Phosphothreonine By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

P29620 [UniParc].

Last modified April 1, 1993. Version 1.
Checksum: 28606BE7120BB048
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FASTA

424

47,613

        10         20         30         40         50         60 
MASGDGGDDA GVKRVADRYL KREVLGEGTY GVVFKAVDTK TGNTVAIKKI RLGKYKEGVN 

        70         80         90        100        110        120 
FTALREIKLL KELKDSNIIE LIDAFPYKGN LHLVFEFMET DLEAVIRDRN IVLSPADTKS 

       130        140        150        160        170        180 
YIQMMLKGLA FCHKKWVLHR DMKPNNLLIG ADGQLKLADF GLARIFGSPE RNFTHQVFAR 

       190        200        210        220        230        240 
WYRAPELLFG TKQYGSAVDI WAAGCIFAEL LLRRPFLQGS SDIDQLGKIF AAFGTPKSSQ 

       250        260        270        280        290        300 
WPDMVYLPDY VEYQFVSAPP LRSLFPMASD DALDLLSRMF TYDPKARITA QQALEHRYFL 

       310        320        330        340        350        360 
SVPAPTKPSQ LPRPPPKGDS GNNKIPDLNL QDGPVVLSPP RKLRRVTAHE GMEVHMHRAD 

       370        380        390        400        410        420 
RTEEHPSGAR HMDDMSSQSS RIPMSVDVGA IFGTRPAPRP TLNSADKSRL KRKLDMDPEF 


GYTE

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"A fine physical map of the rice chromosome 5." Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J., Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F., Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y. Mol. Genet. Genomics 274:337-345(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.
[3]	"The map-based sequence of the rice genome." International rice genome sequencing project (IRGSP) Nature 436:793-800(2005) [PubMed] [Europe PMC] [Abstract] 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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X58194 mRNA. Translation: CAA41172.1. AC107085 Genomic DNA. Translation: AAV31263.1. Sequence problems. AP008211 Genomic DNA. Translation: BAF17364.1.
PIR	S13934.
RefSeq	NP_001055450.1. NM_001061985.1.
UniGene	Os.2689.
3D structure databases
ProteinModelPortal	P29620.
SMR	P29620. Positions 21-314.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	LOC_Os05g32600.1; LOC_Os05g32600.1; LOC_Os05g32600.
GeneID	4338689.
KEGG	dosa:Os05t0392300-01. osa:4338689.
Organism-specific databases
Gramene	P29620.
Phylogenomic databases
eggNOG	COG0515.
KO	K02202.
OMA	PRPNCPA.
ProtClustDB	CLSN2679882.
Gene expression databases
ArrayExpress	P29620.
Family and domain databases
InterPro	IPR011009. Kinase-like_dom. IPR000719. Prot_kinase_cat_dom. IPR017441. Protein_kinase_ATP_BS. IPR002290. Ser/Thr_dual-sp_kinase_dom. IPR008271. Ser/Thr_kinase_AS. [Graphical view]
Pfam	PF00069. Pkinase. 1 hit. [Graphical view]
SMART	SM00220. S_TKc. 1 hit. [Graphical view]
SUPFAM	SSF56112. Kinase_like. 1 hit.
PROSITE	PS00107. PROTEIN_KINASE_ATP. 1 hit. PS50011. PROTEIN_KINASE_DOM. 1 hit. PS00108. PROTEIN_KINASE_ST. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

CDKD1_ORYSJ

Accession

Primary (citable) accession number: P29620
Secondary accession number(s): Q0DIF9, Q60ES0

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1993
Last sequence update:	April 1, 1993
Last modified:	May 1, 2013
This is version 101 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program

Relevant documents

Oryza sativa (rice)

Index of Oryza sativa entries and their corresponding gene designations

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents