O15516 (CLOCK_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified April 16, 2014. Version 144. History...
Names and origin
|Protein names||Recommended name:|
Circadian locomoter output cycles protein kaput
Class E basic helix-loop-helix protein 8
|Organism||Homo sapiens (Human) [Reference proteome]|
|Taxonomic identifier||9606 [NCBI]|
|Taxonomic lineage||Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo|
|Sequence length||846 AA.|
|Protein existence||Evidence at protein level|
General annotation (Comments)
Transcriptional activator which forms a core component of the circadian clock. The circadian clock, an internal time-keeping system, regulates various physiological processes through the generation of approximately 24 hour circadian rhythms in gene expression, which are translated into rhythms in metabolism and behavior. It is derived from the Latin roots 'circa' (about) and 'diem' (day) and acts as an important regulator of a wide array of physiological functions including metabolism, sleep, body temperature, blood pressure, endocrine, immune, cardiovascular, and renal function. Consists of two major components: the central clock, residing in the suprachiasmatic nucleus (SCN) of the brain, and the peripheral clocks that are present in nearly every tissue and organ system. Both the central and peripheral clocks can be reset by environmental cues, also known as Zeitgebers (German for 'timegivers'). The predominant Zeitgeber for the central clock is light, which is sensed by retina and signals directly to the SCN. The central clock entrains the peripheral clocks through neuronal and hormonal signals, body temperature and feeding-related cues, aligning all clocks with the external light/dark cycle. Circadian rhythms allow an organism to achieve temporal homeostasis with its environment at the molecular level by regulating gene expression to create a peak of protein expression once every 24 hours to control when a particular physiological process is most active with respect to the solar day. Transcription and translation of core clock components (CLOCK, NPAS2, ARNTL/BMAL1, ARNTL2/BMAL2, PER1, PER2, PER3, CRY1 and CRY2) plays a critical role in rhythm generation, whereas delays imposed by post-translational modifications (PTMs) are important for determining the period (tau) of the rhythms (tau refers to the period of a rhythm and is the length, in time, of one complete cycle). A diurnal rhythm is synchronized with the day/night cycle, while the ultradian and infradian rhythms have a period shorter and longer than 24 hours, respectively. Disruptions in the circadian rhythms contribute to the pathology of cardiovascular diseases, cancer, metabolic syndromes and aging. A transcription/translation feedback loop (TTFL) forms the core of the molecular circadian clock mechanism. Transcription factors, CLOCK or NPAS2 and ARNTL/BMAL1 or ARNTL2/BMAL2, form the positive limb of the feedback loop, act in the form of a heterodimer and activate the transcription of core clock genes and clock-controlled genes (involved in key metabolic processes), harboring E-box elements (5'-CACGTG-3') within their promoters. The core clock genes: PER1/2/3 and CRY1/2 which are transcriptional repressors form the negative limb of the feedback loop and interact with the CLOCK|NPAS2-ARNTL/BMAL1|ARNTL2/BMAL2 heterodimer inhibiting its activity and thereby negatively regulating their own expression. This heterodimer also activates nuclear receptors NR1D1, NR1D2, RORA, RORB and RORG, which form a second feedback loop and which activate and repress ARNTL/BMAL1 transcription, respectively. CLOCK has an intrinsic acetyltransferase activity, which enables circadian chromatin remodeling by acetylating histones and nonhistone proteins, including its own partner ARNTL/BMAL1. Regulates the circadian expression of ICAM1, VCAM1, CCL2, THPO and MPL and also acts as an enhancer of the transactivation potential of NF-kappaB. The CLOCK-ARNTL/BMAL1 heterodimer regulates the circadian expression of SERPINE1/PAI1, VWF, B3, CCRN4L/NOC, NAMPT, DBP, MYOD1, PPARGC1A, PPARGC1B, SIRT1, GYS2 and also genes implicated in glucose and lipid metabolism. Represses glucocorticoid receptor (GR)-induced transcriptional activity by reducing the association of GR to glucocorticoid response elements (GREs) via the acetylation of multiple lysine residues located in its hinge region. Promotes rhythmic chromatin opening, regulating the DNA accessibility of other transcription factors. Ref.8 Ref.9 Ref.10 Ref.11 Ref.16
Acetyl-CoA + [histone] = CoA + acetyl-[histone].
Component of the circadian clock oscillator which includes the CRY proteins, CLOCK or NPAS2, ARNTL/BMAL1 or ARNTL2/BMAL2, CSNK1D and/or CSNK1E, TIMELESS and the PER proteins. Efficient DNA binding requires dimerization with another bHLH protein. Forms a heterodimer with ARNTL/BMAL1 and this heterodimerization is required for E-box-dependent transactivation, for CLOCK nuclear translocation and degradation, and for phosphorylation of both CLOCK and ARNTL/BMAL1. Interaction with PER and CRY proteins requires translocation to the nucleus. Interaction of the CLOCK-ARNTL/BMAL1 heterodimer with PER or CRY inhibits transcription activation. Interacts with CIPC. Interacts with NR3C1 in a ligand-dependent fashion. Interacts with RELA/p65, EIF4E, PIWIL1, DDX4, PER2 and MGEA5. The CLOCK-ARNTL/BMAL1 heterodimer interacts with GSK3B By similarity. Interacts with ESR1 and estrogen stimulates this interaction. Interacts with the complex p35/CDK5. Ref.9 Ref.13 Ref.14
Nucleus. Chromosome. Cytoplasm By similarity. Nucleus By similarity. Note: Shuffling between the cytoplasm and the nucleus is under circadian regulation and is ARNTL/BMAL1-dependent. Phosphorylated form located in the nucleus while the nonphosphorylated form found only in the cytoplasm By similarity. Localizes to sites of DNA damage in a H2AX-independent manner. Ref.10 Ref.14
Hair follicles (at protein level). Expressed in all tissues examined including spleen, thymus, prostate, testis, ovary, small intestine, colon, leukocytes, heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. Highest levels in testis and skeletal muscle. Low levels in thymus, lung and liver. Expressed in all brain regions with highest levels in cerebellum. Highly expressed in the suprachiasmatic nucleus (SCN). Ref.1 Ref.16
Ubiquitinated, leading to its proteasomal degradation By similarity.
O-glycosylated; contains O-GlcNAc. O-glycosylation by OGT prevents protein degradation by inhibiting ubiquitination. It also stabilizes the CLOCK-ARNTL/BMAL1 heterodimer thereby increasing CLOCK-ARNTL/BMAL1-mediated transcriptional activation of PER1/2/3 and CRY1/2 By similarity.
Phosphorylation is dependent on the CLOCK-ARNTL/BMAL1 heterodimer formation. Phosphorylation enhances the transcriptional activity, alters the subcellular localization and decreases the stability of the heterodimer by promoting its degradation.
Sumoylation enhances its transcriptional activity and interaction with ESR1, resulting in up-regulation of ESR1 activity. Estrogen stimulates sumoylation. Desumoylation by SENP1 negatively regulates its transcriptional activity. Sumoylation stimulates cell proliferation and increases the proportion of S phase cells in breast cancer cell lines. Ref.14
CLOCK-ARNTL/BMAL1 double mutations within the PAS domains result in syngernistic desensitization to high levels of CRY on repression of CLOCK-ARNTL/BMAl1 transcriptional activity of PER1 and disrupt circadian rhythmicity.
Contains 1 bHLH (basic helix-loop-helix) domain.
Contains 1 PAC (PAS-associated C-terminal) domain.
Contains 2 PAS (PER-ARNT-SIM) domains.
The sequence BAA20792.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.
Sequence annotation (Features)
|Feature key||Position(s)||Length||Description||Graphical view||Feature identifier|
|Chain||1 – 846||846||Circadian locomoter output cycles protein kaput||PRO_0000127163|
|Domain||34 – 84||51||bHLH|
|Domain||107 – 177||71||PAS 1|
|Domain||262 – 332||71||PAS 2|
|Domain||336 – 379||44||PAC|
|Region||371 – 845||475||Interaction with NR3C1 By similarity|
|Region||514 – 564||51||Implicated in the circadian rhythmicity By similarity|
|Motif||32 – 47||16||Nuclear localization signal By similarity|
|Compositional bias||744 – 760||17||Gln-rich|
|Compositional bias||819 – 828||10||Poly-Gln|
Amino acid modifications
|Modified residue||38||1||Phosphoserine By similarity|
|Modified residue||42||1||Phosphoserine By similarity|
|Modified residue||408||1||Phosphoserine By similarity|
|Modified residue||427||1||Phosphoserine; by GSK3-beta By similarity|
|Modified residue||451||1||Phosphothreonine; by CDK5 Ref.13|
|Modified residue||461||1||Phosphothreonine; by CDK5 Ref.13|
|Cross-link||67||Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)|
|Cross-link||842||Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1) By similarity|
|Natural variant||208||1||S → C.|
Corresponds to variant rs34897046 [ dbSNP | Ensembl ].
|Natural variant||380||1||E → K.|
Corresponds to variant rs1056478 [ dbSNP | Ensembl ].
|Natural variant||395||1||L → I.|
Corresponds to variant rs6855837 [ dbSNP | Ensembl ].
|Natural variant||542||1||H → R.|
Corresponds to variant rs3762836 [ dbSNP | Ensembl ].
|Mutagenesis||116||1||E → K: 3-fold increase in PER1 reporter activity by CLOCK-ARNTL/BMAL1. Some reduction of CRY1 inhibition of CLOCK-ARNTL/BMAL1 transcriptional activity; when associated with K-367 and L-601. Ref.7|
|Mutagenesis||332||1||G → E: 3-fold increase in PER1 reporter activity by CLOCK-ARNTL/BMAL1. Some reduction of CRY1 inhibition of CLOCK-ARNTL/BMAL1 transcriptional activity; when associated with L-840. Ref.7|
|Mutagenesis||360||1||H → Y: 3-fold increase in PER1 reporter activity by CLOCK-ARNTL/BMAL1. Some reduction of CRY1 inhibition of CLOCK-ARNTL/BMAL1 transcriptional activity. Ref.7|
|Mutagenesis||367||1||E → K: 3-fold increase in PER1 reporter activity by CLOCK-ARNTL/BMAL1. Some reduction of CRY1 inhibition CLOCK-ARNTL/BMAL1 transcriptional activity; when associated with E-116 and L-601. Ref.7|
|Mutagenesis||451||1||T → F: Significant loss in phosphorylation. Ref.13|
|Mutagenesis||461||1||T → F: Significant loss in phosphorylation. Ref.13|
|Mutagenesis||601||1||V → L: 3-fold increase in PER1 reporter activity by CLOCK-ARNTL/BMAL1. Some reduction of CRY1 inhibition of CLOCK-ARNTL/BMAL1 transcriptional activity; when associated with K-116 and K-367. Ref.7|
|Mutagenesis||840||1||P → L: 3-fold increase in PER1 reporter activity by CLOCK-ARNTL/BMAL1. Some reduction of CRY1 inhibition of CLOCK-ARNTL/BMAL1 transcriptional activity; when associated with E-332. Ref.7|
|Sequence conflict||440||1||S → P in AAF13733. Ref.1|
Helix Strand Turn
|Helix||33 – 58||26|
|Beta strand||61 – 63||3|
|Helix||70 – 89||20|
|||"Molecular cloning and characterization of the human CLOCK gene: expression in the suprachiasmatic nuclei."|
Steeves T.D.L., King D.P., Zhao Y., Sangoram A.M., Du F., Bowcock A.M., Moore R.Y., Takahashi J.S.
Genomics 57:189-200(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], TISSUE SPECIFICITY.
|||NHLBI resequencing and genotyping service (RS&G)|
Submitted (SEP-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
|||"Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro."|
Nagase T., Ishikawa K., Nakajima D., Ohira M., Seki N., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
DNA Res. 4:141-150(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
|||"Complete sequencing and characterization of 21,243 full-length human cDNAs."|
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
|||"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."|
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
|||"Molecular cloning of human Clock cDNA 5'-end."|
Ikeda M., Takehara N., Ebisawa T., Yamauchi T., Nomura M.
Submitted (AUG-1997) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-349.
|||"Feedback repression is required for mammalian circadian clock function."|
Sato T.K., Yamada R.G., Ukai H., Baggs J.E., Miraglia L.J., Kobayashi T.J., Welsh D.K., Kay S.A., Ueda H.R., Hogenesch J.B.
Nat. Genet. 38:312-319(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF GLU-116; GLY-332; HIS-360; GLU-367; VAL-601 AND PRO-840.
|||"CLOCK/BMAL1 regulates human nocturnin transcription through binding to the E-box of nocturnin promoter."|
Li R., Yue J., Zhang Y., Zhou L., Hao W., Yuan J., Qiang B., Ding J.M., Peng X., Cao J.M.
Mol. Cell. Biochem. 317:169-177(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
|||"Peripheral CLOCK regulates target-tissue glucocorticoid receptor transcriptional activity in a circadian fashion in man."|
Charmandari E., Chrousos G.P., Lambrou G.I., Pavlaki A., Koide H., Ng S.S., Kino T.
PLoS ONE 6:E25612-E25612(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH NR3C1.
|||"A DNA damage response screen identifies RHINO, a 9-1-1 and TopBP1 interacting protein required for ATR signaling."|
Cotta-Ramusino C., McDonald E.R. III, Hurov K., Sowa M.E., Harper J.W., Elledge S.J.
Science 332:1313-1317(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
|||"Diurnal expression of the thrombopoietin gene is regulated by CLOCK."|
Tracey C.J., Pan X., Catterson J.H., Harmar A.J., Hussain M.M., Hartley P.S.
J. Thromb. Haemost. 10:662-669(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
|||"Mechanism of the circadian clock in physiology."|
Richards J., Gumz M.L.
Am. J. Physiol. 304:R1053-R1064(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
|||"Cyclin-dependent kinase 5 (Cdk5) regulates the function of CLOCK protein by direct phosphorylation."|
Kwak Y., Jeong J., Lee S., Park Y.U., Lee S.A., Han D.H., Kim J.H., Ohshima T., Mikoshiba K., Suh Y.H., Cho S., Park S.K.
J. Biol. Chem. 288:36878-36889(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION AT THR-451 AND THR-461, MUTAGENESIS OF THR-451 AND THR-461, INTERACTION WITH THE COMPLEX P35/CDK5.
|||"CLOCK is a substrate of SUMO and sumoylation of CLOCK upregulates the transcriptional activity of estrogen receptor-alpha."|
Li S., Wang M., Ao X., Chang A.K., Yang C., Zhao F., Bi H., Liu Y., Xiao L., Wu H.
Oncogene 32:4883-4891(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: SUMOYLATION, SUBCELLULAR LOCATION, INTERACTION WITH ESR1.
|||"Metabolism and the circadian clock converge."|
Eckel-Mahan K., Sassone-Corsi P.
Physiol. Rev. 93:107-135(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
|||"A meeting of two chronobiological systems: circadian proteins Period1 and BMAL1 modulate the human hair cycle clock."|
Al-Nuaimi Y., Hardman J.A., Biro T., Haslam I.S., Philpott M.P., Toth B.I., Farjo N., Farjo B., Baier G., Watson R.E., Grimaldi B., Kloepper J.E., Paus R.
J. Invest. Dermatol. 134:610-619(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, TISSUE SPECIFICITY.
|||"Molecular architecture of the mammalian circadian clock."|
Partch C.L., Green C.B., Takahashi J.S.
Trends Cell Biol. 24:90-99(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
|+||Additional computationally mapped references.|
|AF011568 mRNA. Translation: AAB83969.1.|
AH008440 Genomic DNA. Translation: AAF13733.1.
EF015897 Genomic DNA. Translation: ABM64208.1.
AB002332 mRNA. Translation: BAA20792.2. Different initiation.
AK291708 mRNA. Translation: BAF84397.1.
BC126157 mRNA. Translation: AAI26158.1.
BC126159 mRNA. Translation: AAI26160.1.
AB005535 mRNA. Translation: BAA21774.1.
|RefSeq||NP_001254772.1. NM_001267843.1. |
3D structure databases
|SMR||O15516. Positions 31-444. |
Protein-protein interaction databases
|BioGrid||114944. 16 interactions.|
|IntAct||O15516. 3 interactions.|
Protocols and materials databases
Genome annotation databases
|Ensembl||ENST00000309964; ENSP00000308741; ENSG00000134852. |
ENST00000381322; ENSP00000370723; ENSG00000134852.
ENST00000513440; ENSP00000426983; ENSG00000134852.
|UCSC||uc003haz.2. human. |
|HGNC||HGNC:2082. CLOCK. |
|MIM||601851. gene. |
Enzyme and pathway databases
|Reactome||REACT_172623. Chromatin organization. |
REACT_24941. Circadian Clock.
Gene expression databases
Family and domain databases
|Gene3D||4.10.280.10. 1 hit. |
|InterPro||IPR011598. bHLH_dom. |
|Pfam||PF00010. HLH. 1 hit. |
PF00989. PAS. 1 hit.
|PRINTS||PR00785. NCTRNSLOCATR. |
|SMART||SM00353. HLH. 1 hit. |
SM00086. PAC. 1 hit.
SM00091. PAS. 2 hits.
|SUPFAM||SSF47459. SSF47459. 1 hit. |
SSF55785. SSF55785. 2 hits.
|PROSITE||PS50888. BHLH. 1 hit. |
PS50112. PAS. 2 hits.
|Accession||Primary (citable) accession number: O15516|
Secondary accession number(s): A0AV01 Q9UIT8
|Entry status||Reviewed (UniProtKB/Swiss-Prot)|
|Annotation program||Chordata Protein Annotation Program|
|Disclaimer||Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.|
Index of protein domains and families
Index of Protein Data Bank (PDB) cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
|Human polymorphisms and disease mutations|
Index of human polymorphisms and disease mutations
|Human entries with polymorphisms or disease mutations|
List of human entries with polymorphisms or disease mutations
|Human chromosome 4|
Human chromosome 4: entries, gene names and cross-references to MIM