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Circadian locomoter output cycles protein kaput

 CLOCK_CHICK             Reviewed;         875 AA.
Q8QGQ6; Q9W6Q2; Q9W7C3;
28-NOV-2006, integrated into UniProtKB/Swiss-Prot.
28-NOV-2006, sequence version 2.
20-JUN-2018, entry version 112.
RecName: Full=Circadian locomoter output cycles protein kaput;
Name=CLOCK;
Gallus gallus (Chicken).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes;
Phasianidae; Phasianinae; Gallus.
NCBI_TaxID=9031;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY, AND
INDUCTION.
TISSUE=Retina;
PubMed=10407173; DOI=10.1016/S0169-328X(99)00154-0;
Larkin P., Baehr W., Semple-Rowland S.L.;
"Circadian regulation of iodopsin and clock is altered in the retinal
degeneration chicken retina.";
Brain Res. Mol. Brain Res. 70:253-263(1999).
[2]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, INTERACTION WITH
ARNTL, INDUCTION, AND TISSUE SPECIFICITY.
PubMed=10931848; DOI=10.1074/jbc.M005671200;
Chong N.W., Bernard M., Klein D.C.;
"Characterization of the chicken serotonin N-acetyltransferase gene.
Activation via clock gene heterodimer/E box interaction.";
J. Biol. Chem. 275:32991-32998(2000).
[3]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, TISSUE SPECIFICITY,
INDUCTION, AND INTERACTION WITH ARNTL AND ARNTL2.
TISSUE=Pineal gland;
PubMed=11554928; DOI=10.1046/j.1365-2443.2001.00462.x;
Okano T., Yamamoto K., Okano K., Hirota T., Kasahara T., Sasaki M.,
Takanaka Y., Fukada Y.;
"Chicken pineal clock genes: implication of BMAL2 as a bidirectional
regulator in circadian clock oscillation.";
Genes Cells 6:825-836(2001).
[4]
FUNCTION, TISSUE SPECIFICITY, AND INDUCTION.
PubMed=20345751; DOI=10.1111/j.1471-4159.2010.06698.x;
Haque R., Ali F.G., Biscoglia R., Abey J., Weller J., Klein D.,
Iuvone P.M.;
"CLOCK and NPAS2 have overlapping roles in the circadian oscillation
of arylalkylamine N-acetyltransferase mRNA in chicken cone
photoreceptors.";
J. Neurochem. 113:1296-1306(2010).
-!- FUNCTION: 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 NR1D1/2 and RORA/B/G, which form a second
feedback loop and which activate and repress ARNTL/BMAL1
transcription, respectively. CLOCK regulates the circadian
expression of AANAT in the retinal photoreceptor cells. The
preferred binding motif for the CLOCK-ARNTL/BMAL1 heterodimer is
5'-CACGTGA-3', which contains a flanking Ala residue in addition
to the canonical 6-nucleotide E-box sequence (By similarity).
CLOCK specifically binds to the half-site 5'-CAC-3', while ARNTL
binds to the half-site 5'-GTGA-3' (By similarity).
{ECO:0000250|UniProtKB:O08785, ECO:0000269|PubMed:10931848,
ECO:0000269|PubMed:11554928, ECO:0000269|PubMed:20345751}.
-!- SUBUNIT: 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
(By similarity). Forms a heterodimer with ARNTL/BMAL1
(PubMed:10931848). The CLOCK-ARNTL/BMAL1 heterodimer is required
for E-box-dependent transactivation, for CLOCK nuclear
translocation and degradation, and for phosphorylation of both
CLOCK and ARNTL/BMAL1 (By similarity). Interaction with PER and
CRY proteins requires translocation to the nucleus (By
similarity). Interaction of the CLOCK-ARNTL/BMAL1 heterodimer with
PER or CRY inhibits transcription activation (By similarity).
Interacts with ARNTL2/BMAL2 (PubMed:11554928).
{ECO:0000250|UniProtKB:O08785, ECO:0000269|PubMed:10931848,
ECO:0000269|PubMed:11554928}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:O08785}.
Nucleus {ECO:0000255|PROSITE-ProRule:PRU00981}. Cytoplasm, cytosol
{ECO:0000250|UniProtKB:O15516}. Note=Shuffling between the
cytoplasm and the nucleus is under circadian regulation and is
ARNTL/BMAL1-dependent. {ECO:0000250|UniProtKB:O08785}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q8QGQ6-1; Sequence=Displayed;
Name=2;
IsoId=Q8QGQ6-2; Sequence=VSP_021796;
-!- TISSUE SPECIFICITY: Expressed in the retinal photoreceptor cells
(at protein level). Isoform 1 is expressed in both the retina and
pineal gland. Isoform 2 is expressed mainly in the pineal gland.
{ECO:0000269|PubMed:10407173, ECO:0000269|PubMed:10931848,
ECO:0000269|PubMed:11554928, ECO:0000269|PubMed:20345751}.
-!- INDUCTION: Expressed in a circadian rhythm manner in the retina.
Levels increase over daylight hours, reaching maximum levels
between ZT12 and ZT18. Expression levels continue to oscillate
during constant darkness, with levels increasing during subjective
day to reach maximum levels between day/night transition. In the
pineal gland, shows no robust circadian rhythm with only a slight
increase in expression between ZT10-18.
{ECO:0000269|PubMed:10407173, ECO:0000269|PubMed:10931848,
ECO:0000269|PubMed:11554928, ECO:0000269|PubMed:20345751}.
-!- PTM: Ubiquitinated, leading to its proteasomal degradation.
{ECO:0000250|UniProtKB:O08785}.
-!- PTM: 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. {ECO:0000250|UniProtKB:O08785}.
-!- PTM: 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. {ECO:0000250|UniProtKB:O08785}.
-!- PTM: 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.
{ECO:0000250|UniProtKB:O08785}.
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EMBL; AF132531; AAD43283.1; -; mRNA.
EMBL; AF144425; AAD32860.1; -; mRNA.
EMBL; AF246959; AAL98708.1; -; mRNA.
RefSeq; NP_001276763.1; NM_001289834.1.
RefSeq; NP_989505.2; NM_204174.3.
UniGene; Gga.2707; -.
ProteinModelPortal; Q8QGQ6; -.
SMR; Q8QGQ6; -.
STRING; 9031.ENSGALP00000022354; -.
PaxDb; Q8QGQ6; -.
GeneID; 373991; -.
KEGG; gga:373991; -.
CTD; 9575; -.
eggNOG; ENOG410IQ5V; Eukaryota.
eggNOG; ENOG410Y7Z8; LUCA.
HOGENOM; HOG000234382; -.
HOVERGEN; HBG050997; -.
InParanoid; Q8QGQ6; -.
KO; K02223; -.
OrthoDB; EOG091G11CV; -.
PhylomeDB; Q8QGQ6; -.
PRO; PR:Q8QGQ6; -.
Proteomes; UP000000539; Unplaced.
Bgee; ENSGALG00000013793; -.
GO; GO:0005829; C:cytosol; ISS:UniProtKB.
GO; GO:0005634; C:nucleus; ISS:UniProtKB.
GO; GO:0005667; C:transcription factor complex; IEA:InterPro.
GO; GO:0003677; F:DNA binding; ISS:UniProtKB.
GO; GO:0003700; F:DNA binding transcription factor activity; IEA:InterPro.
GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
GO; GO:0000980; F:RNA polymerase II distal enhancer sequence-specific DNA binding; IDA:UniProtKB.
GO; GO:0006974; P:cellular response to DNA damage stimulus; IEA:UniProtKB-KW.
GO; GO:0032922; P:circadian regulation of gene expression; IMP:UniProtKB.
GO; GO:0006473; P:protein acetylation; ISS:UniProtKB.
GO; GO:0051775; P:response to redox state; ISS:UniProtKB.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
CDD; cd00083; HLH; 1.
CDD; cd00130; PAS; 2.
Gene3D; 4.10.280.10; -; 1.
InterPro; IPR011598; bHLH_dom.
InterPro; IPR036638; HLH_DNA-bd_sf.
InterPro; IPR001067; Nuc_translocat.
InterPro; IPR001610; PAC.
InterPro; IPR000014; PAS.
InterPro; IPR035965; PAS-like_dom_sf.
InterPro; IPR013767; PAS_fold.
Pfam; PF00010; HLH; 1.
Pfam; PF00989; PAS; 1.
PRINTS; PR00785; NCTRNSLOCATR.
SMART; SM00353; HLH; 1.
SMART; SM00086; PAC; 1.
SMART; SM00091; PAS; 2.
SUPFAM; SSF47459; SSF47459; 1.
SUPFAM; SSF55785; SSF55785; 2.
PROSITE; PS50888; BHLH; 1.
PROSITE; PS50112; PAS; 2.
1: Evidence at protein level;
Activator; Alternative splicing; Biological rhythms;
Complete proteome; Cytoplasm; DNA damage; DNA-binding;
Isopeptide bond; Nucleus; Phosphoprotein; Reference proteome; Repeat;
Transcription; Transcription regulation; Ubl conjugation.
CHAIN 1 875 Circadian locomoter output cycles protein
kaput.
/FTId=PRO_0000262642.
DOMAIN 34 84 bHLH. {ECO:0000255|PROSITE-
ProRule:PRU00981}.
DOMAIN 107 177 PAS 1. {ECO:0000255|PROSITE-
ProRule:PRU00140}.
DOMAIN 262 332 PAS 2. {ECO:0000255|PROSITE-
ProRule:PRU00140}.
DOMAIN 336 379 PAC.
REGION 516 566 Implicated in the circadian rhythmicity.
{ECO:0000250}.
MOTIF 32 47 Nuclear localization signal.
{ECO:0000250|UniProtKB:O08785}.
COMPBIAS 483 857 Gln-rich.
SITE 39 39 Interaction with E-box DNA.
{ECO:0000250|UniProtKB:O15516}.
SITE 43 43 Interaction with E-box DNA.
{ECO:0000250|UniProtKB:O15516}.
SITE 47 47 Interaction with E-box DNA.
{ECO:0000250|UniProtKB:O15516}.
SITE 84 84 Important for interaction with
ARNTL/BMAL1.
{ECO:0000250|UniProtKB:O15516}.
MOD_RES 38 38 Phosphoserine.
{ECO:0000250|UniProtKB:O08785}.
MOD_RES 42 42 Phosphoserine.
{ECO:0000250|UniProtKB:O08785}.
MOD_RES 408 408 Phosphoserine.
{ECO:0000250|UniProtKB:O08785}.
MOD_RES 427 427 Phosphoserine; by GSK3-beta.
{ECO:0000250|UniProtKB:O08785}.
MOD_RES 451 451 Phosphothreonine; by CDK5.
{ECO:0000250|UniProtKB:O08785}.
MOD_RES 461 461 Phosphothreonine; by CDK5.
{ECO:0000250|UniProtKB:O08785}.
CROSSLNK 67 67 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO1).
{ECO:0000250|UniProtKB:O08785}.
CROSSLNK 871 871 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO1).
{ECO:0000250|UniProtKB:O08785}.
VAR_SEQ 567 585 Missing (in isoform 2).
{ECO:0000303|PubMed:10407173,
ECO:0000303|PubMed:10931848,
ECO:0000303|PubMed:11554928}.
/FTId=VSP_021796.
CONFLICT 105 105 L -> P (in Ref. 1; AAD43283).
{ECO:0000305}.
CONFLICT 160 160 E -> Q (in Ref. 2; AAD32860).
{ECO:0000305}.
CONFLICT 217 217 G -> D (in Ref. 1; AAD43283).
{ECO:0000305}.
CONFLICT 507 507 L -> H (in Ref. 1; AAD43283).
{ECO:0000305}.
CONFLICT 514 517 Missing (in Ref. 2; AAD32860).
{ECO:0000305}.
CONFLICT 785 785 Q -> QQ (in Ref. 2; AAD32860).
{ECO:0000305}.
CONFLICT 796 796 Q -> QQ (in Ref. 3; AAL98708).
{ECO:0000305}.
SEQUENCE 875 AA; 98659 MW; BFC79C9E610DAE1E CRC64;
MFFTISTHKM SSIADRNDGS IFDGLVEEDD KDKAKRVSRN KSEKKRRDQF NVLIKELGSM
LPGNARKMDK STVLQKSIDF LRKHKEITAQ SDASEIRQDW KPTFLSNEEF TQLMLEALDG
FFLAIMTDGN IIYVSESVTP LLEHLPSDLV DQSVFNFIPE GEHSEIYKIL SSHLLESDSL
TPEYLKSKNQ LEFCCHMLRG TIDPKEQPTY EYVKFIGNFK CLNNVPNSAH NGFEGTIQRS
HRPSYEDKVC FIATVRLATP QFIKEMCTVE EPNEEFTSRH SLEWKFLFLD HRAPPIIGYL
PFEVLGTSGY DYYHVDDLDN LAKCHEHLMQ YGKGKSCYYR FLTKGQQWIW LQTHYYITYH
QWNSRPEFIV CTHTVVSYAE VRAERRRELG IEESLPEIKA DKSQDSGSDN HINTVSLKEA
LERFDTSPTP SASSRSSRKS SHTAVSDHSS TPTKMTVDTS TPPRQSLSAH EKSTQRRSSL
SSQSLSSQSL GQPVTQPTMS QPATLQLQSS MSQPVFQFSA QLGAMQHLKD QLEQRTRMIE
ANIHRQQEEL RKIQEQLQIV HGQGLQLSSG PCVPKIHRTD VTVPEMFLQQ STSGLNFSSV
QLTSGNSSSV QQLAPGNMQG QVVQTNQTQS GMNTGHTSTP HMIQQQPLQS SASQHNQQNV
LSGHGQQSSL AGQSQNTVST PLYNTMVISQ PTAGNVVQVP SSLPQNNNQN AAAVTTFTQD
RQIRFSQGQQ LVTKLVTAPV ACGAVMVPST MFMGQVVTAY PTFAAQQQQP QTLPVTQQQQ
QQQQQSQQDQ QQQQQQLTAV QQPAQPQLTQ HPQQFLQTSR LLHGNQSAQL ILSAAFPLQQ
STFTQSHHQQ HQPQQQQLSR HRTDKMTDPS KAQPQ


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