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Q9WVS9 (CLOCK_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 94. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Circadian locomoter output cycles protein kaput
Short name=rCLOCK
EC=2.3.1.48
Gene names
Name:Clock
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length862 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

ARNTL/2-CLOCK heterodimers activate E-box element (5'-CACGTG-3') transcription of a number of proteins of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback loop by PER and CRY proteins. Has intrinsic histone acetyltransferase activity and this enzymatic function contributes to chromatin-remodeling events implicated in circadian control of gene expression. Acetylates primarily histones H3 and H4. Acetylates also a non-histone substrate: ARNTL. Plays a role in DNA damage response (DDR) signaling during the S phase By similarity.

Catalytic activity

Acetyl-CoA + [histone] = CoA + acetyl-[histone].

Subunit structure

Component of the circadian clock oscillator which includes the CRY proteins, CLOCK or NPAS2, ARNTL or ARNTL2, CSNK1D and/or CSNK1E, TIMELESS and the PER proteins. Efficient DNA binding requires dimerization with another bHLH protein. Heterodimerization with ARNTL is required for E-box-dependent transactivation, for CLOCK nuclear translocation and degradation, and, for phosphorylation of both CLOCK and ARNTL. Interaction with PER and CRY proteins requires translocation to the nucleus. Interaction of the CLOCK-ARNTL heterodimer with PER or CRY inhibits transcription activation. Binds weakly ARNTL and ARNTL2 to form heterodimers which bind poorly to the E-box motif By similarity.

Subcellular location

Cytoplasm By similarity. Nucleus By similarity. Chromosome By similarity. Note: Localizes to sites of DNA damage in a H2AX-independent manner. Shuffling between the cytoplasm and the nucleus is under circadian regulation and is ARNTL-dependent By similarity.

Tissue specificity

Expressed in the suprachiasmatic nucleus (SCN), and in the piriform cortex (PC). Ref.1

Induction

Without light exposure, high levels at ZT6 and low levels at ZT18 and ZT22. Light exposure increases levels in the SCN in phase dependent manner. Levels increased significantly during the subjective night (ZT10-20). In the piriform cortex, levels increased by light at ZT14. Ref.1

Post-translational modification

Phosphorylation is dependent on CLOCK-ARNTL heterodimer formation By similarity.

Sequence similarities

Contains 1 bHLH (basic helix-loop-helix) domain.

Contains 1 PAC (PAS-associated C-terminal) domain.

Contains 2 PAS (PER-ARNT-SIM) domains.

Ontologies

Keywords
   Biological processBiological rhythms
DNA damage
Transcription
Transcription regulation
   Cellular componentChromosome
Cytoplasm
Nucleus
   Coding sequence diversityAlternative splicing
   DomainRepeat
   LigandDNA-binding
   Molecular functionActivator
Transferase
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcircadian regulation of gene expression

Inferred from sequence or structural similarity. Source: UniProtKB

entrainment of circadian clock

Inferred from expression pattern Ref.1. Source: RGD

histone acetylation

Inferred from electronic annotation. Source: GOC

response to DNA damage stimulus

Inferred from electronic annotation. Source: UniProtKB-KW

transcription, DNA-dependent

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentchromosome

Inferred from electronic annotation. Source: UniProtKB-SubCell

cytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

transcription factor complex

Inferred from sequence or structural similarity. Source: UniProtKB

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

histone acetyltransferase activity

Inferred from electronic annotation. Source: EC

sequence-specific DNA binding transcription factor activity

Inferred from sequence or structural similarity. Source: UniProtKB

signal transducer activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9WVS9-1)

Also known as: Long; Clock-L;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q9WVS9-2)

Also known as: Short; Clock-S;

The sequence of this isoform differs from the canonical sequence as follows:
     484-513: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 862862Circadian locomoter output cycles protein kaput
PRO_0000262638

Regions

Domain34 – 8451bHLH
Domain107 – 17771PAS 1
Domain262 – 33271PAS 2
Domain336 – 37944PAC
Region514 – 56451Implicated in the circadian rhythmicity By similarity
Compositional bias483 – 844362Gln-rich

Amino acid modifications

Modified residue4081Phosphoserine By similarity

Natural variations

Alternative sequence484 – 51330Missing in isoform 2.
VSP_021795

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (Long) (Clock-L) [UniParc].

Last modified November 1, 1999. Version 1.
Checksum: D031E4A3758907EC

FASTA86297,004
        10         20         30         40         50         60 
MLFTVSCSKM SSIVDRDDSS IFDGLVEEDD KDKAKRVSRN KSEKKRRDQF NVLIKELGSM 

        70         80         90        100        110        120 
LPGNARKMDK STVLQKSIDF LRKHKEITAQ SDASEIRQDW KPTFLSNEEF TQLMLEALDG 

       130        140        150        160        170        180 
FFLAIMTDGS IIYVSETVTS LLEHLPSDLV DQSIFNFIPE GEHSEVYKIL STHLLESDSL 

       190        200        210        220        230        240 
TPEDLKSKNQ LEFCCHMLRG TIDPKEPSTY EYVRFIGNFK SLNSVSTSTH NGFEGTIQRT 

       250        260        270        280        290        300 
HRPSYEDRVC FVATVRLATP QFIKEMCTVE EPNEEFTSRH SLEWKFLFLD HRAPPIIGYL 

       310        320        330        340        350        360 
PFEVLGTSGY DYYHVDDLES LAKCHEHLMQ YGKGKSCYYR FLTKGQQWIW LQTHYYITYH 

       370        380        390        400        410        420 
QWNSRPEFIV CTHTVVSYAE VRAERRRELG VEESLPETAA DKSQDSGSDN RINTVSLKEA 

       430        440        450        460        470        480 
LERFDHSPTP SASSRSSRKS SHTAVSDPSS TPTKIPTDTS TPPRPHLPAH EKMTQRRSSF 

       490        500        510        520        530        540 
SSQSINSQSV GSSLTQPAMS QAANLPIPQG MSQFQLSAQL GAMQHLKDQL EQRTRMIEAN 

       550        560        570        580        590        600 
IHRQQEELRK IQEQLQMVHG QGLQMFLQQS NPGLNLGSVQ LSSGNSNIQQ LTPINMQGQV 

       610        620        630        640        650        660 
VPVNQIQSGV NAGHVSTGQH MIQQQTLQST STQSQQSVMS GHSQPTSLPN QTPSTLTAPL 

       670        680        690        700        710        720 
YNTMVISQPA AGSMVPIPSS MPQNSTQSAT VTTFTQDRQI RFSQGQQLVT KLVTAPVACG 

       730        740        750        760        770        780 
AVMVPSTMLM GQVVTAYPTF ATQQQQAQAL SVTQQQQQQQ QQQQQQQQQQ PQQAQQPQSQ 

       790        800        810        820        830        840 
QSSQDQPHPS VQQPAQLTQP PQQFLQTSRL LHGNPSTQLI LSAAFPLQQS TFPPSHHQQH 

       850        860 
QQQQLHRHRT DSLTDPSKVQ PQ

« Hide

Isoform 2 (Short) (Clock-S) [UniParc].

Checksum: 60AD1E3031406FB9
Show »

FASTA83293,991

References

[1]"Phase-dependent induction by light of rat Clock gene expression in the suprachiasmatic nucleus."
Abe H., Honma S., Namihira M., Tanahashi Y., Ikeda M., Yu W., Honma K.
Brain Res. Mol. Brain Res. 66:104-110(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY, INDUCTION.
Tissue: Brain.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AB019258 mRNA. Translation: BAA81819.1.
AB019259 mRNA. Translation: BAB68768.1.
IPIIPI00201128.
IPI00205319.
RefSeqNP_068628.1. NM_021856.1.
UniGeneRn.205839.

3D structure databases

HSSPHSSP built from PDB template 1AM9 based on UniProtKB P36956.
ProteinModelPortalQ9WVS9.
ModBaseSearch...

PTM databases

PhosphoSiteQ9WVS9.

Proteomic databases

PaxDbQ9WVS9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID60447.
KEGGrno:60447.
UCSCRGD:620271. rat.

Organism-specific databases

CTD9575.
RGD620271. Clock.

Phylogenomic databases

eggNOGNOG300360.
HOGENOMHOG000234382.
HOVERGENHBG050997.
InParanoidQ9WVS9.
KOK02223.

Gene expression databases

ArrayExpressQ9WVS9.
GenevestigatorQ9WVS9.
GermOnlineENSRNOG00000002175. Rattus norvegicus.

Family and domain databases

Gene3D4.10.280.10. 1 hit.
InterProIPR011598. bHLH_dom.
IPR001067. Nuc_translocat.
IPR001610. PAC.
IPR000014. PAS.
IPR013767. PAS_fold.
IPR013655. PAS_fold_3.
[Graphical view]
PfamPF00010. HLH. 1 hit.
PF00989. PAS. 1 hit.
PF08447. PAS_3. 1 hit.
[Graphical view]
PRINTSPR00785. NCTRNSLOCATR.
SMARTSM00353. HLH. 1 hit.
SM00086. PAC. 1 hit.
SM00091. PAS. 2 hits.
[Graphical view]
SUPFAMSSF47459. HLH_basic. 1 hit.
PROSITEPS50888. BHLH. 1 hit.
PS50113. PAC. False negative.
PS50112. PAS. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

NextBio612192.

Entry information

Entry nameCLOCK_RAT
AccessionPrimary (citable) accession number: Q9WVS9
Secondary accession number(s): Q920Y1
Entry history
Integrated into UniProtKB/Swiss-Prot: November 28, 2006
Last sequence update: November 1, 1999
Last modified: May 1, 2013
This is version 94 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

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