Circadian clock protein kinase KaiC - Synechococcus elongatus (strain PCC 7942)

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Q79PF4 (KAIC_SYNE7) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 85. History...

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

Documents (2) |

Third-party data

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

Names and origin

Protein names

Recommended name:
Circadian clock protein kinase KaiC
EC=2.7.11.1

Gene names

Name:	kaiC
Ordered Locus Names:	Synpcc7942_1216
ORF Names:	see0011

Organism

Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2) [Complete proteome] [HAMAP]

Taxonomic identifier

1140 [NCBI]

Taxonomic lineage

Bacteria › Cyanobacteria › Oscillatoriophycideae › Chroococcales › Synechococcus ›

Protein attributes

Sequence length	519 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Core component of the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. Binds to DNA. The KaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction. Ref.1 Ref.12
Catalytic activity	ATP + a protein = ADP + a phosphoprotein. HAMAP-Rule MF_01836
Cofactor	Magnesium. Ref.15
Enzyme regulation	The interaction with KaiA enhances its phosphorylation status, while the interaction with KaiB decreases it. A KaiA dimer is sufficient to enhance KaiC phosphorylation. Ref.8 Ref.10 Ref.11
Subunit structure	Homohexamer; hexamerization is dependent on ATP-binding. Core component of the KaiABC complex, at least composed of a KaiC homohexamer, a KaiB dimer and two KaiA dimers. Interacts directly with SasA. Ref.4 Ref.6 Ref.7 Ref.9 Ref.10 Ref.11
Developmental stage	Accumulates in a circadian fashion, peaking at circadian time (CT) 15-18. Ref.14
Induction	Down-regulated by itself. Ref.8 Ref.10 Ref.11 Ref.12
Domain	The KaiC domains mediate the interaction with KaiA. HAMAP-Rule MF_01836
Post-translational modification	Phosphorylated on serine/threonine residues by autocatalysis. Both phosphorylated and unphosphorylated forms exist. Can probably autophosphorylate and autodephosphorylate. Phosphorylated form correlates with clock speed. Ref.5 Ref.8 Ref.10 Ref.11
Miscellaneous	'Kai' means 'cycle' in Japanese. HAMAP-Rule MF_01836
Sequence similarities	Belongs to the KaiC family. Contains 2 kaiC domains.

Ontologies

Keywords
Biological process	Biological rhythms Transcription Transcription regulation
Domain	Repeat
Ligand	ATP-binding DNA-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Repressor Serine/threonine-protein kinase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological_process	circadian rhythm Inferred from electronic annotation. Source: HAMAP entrainment of circadian clock Inferred from direct assay Ref.4. Source: UniProtKB negative regulation of circadian rhythm Traceable author statement Ref.7. Source: UniProtKB regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP DNA binding Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: HAMAP protein serine/threonine kinase activity Inferred from electronic annotation. Source: UniProtKB-KW protein serine/threonine/tyrosine kinase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct
itself		10	EBI-592287,EBI-592287
kaiA	Q79PF6	17	EBI-592287,EBI-592281
kaiB	Q79PF5	10	EBI-592287,EBI-619150
sasA	Q06904	6	EBI-592287,EBI-626872

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 519

519

Circadian clock protein kinase KaiC HAMAP-Rule MF_01836

PRO_0000217782

Regions

Domain

19 – 260

242

KaiC 1

Domain

261 – 493

233

KaiC 2

Nucleotide binding

46 – 53

ATP HAMAP-Rule MF_01836

Nucleotide binding

288 – 295

ATP HAMAP-Rule MF_01836

Sites

Metal binding

295

Magnesium

Metal binding

318

Magnesium

Metal binding

319

Magnesium

Metal binding

378

Magnesium

Amino acid modifications

Modified residue

432

Phosphothreonine; by autocatalysis HAMAP-Rule MF_01836

Experimental info

Mutagenesis

K → A: Induces an arrhythmic phenotype. Ref.5

Mutagenesis

G → A: Lowers the amplitude and distords the waveform of the circadian rhythm. Ref.5

Mutagenesis

A → V in kaiC1; shortens the period of the circadian rhythm to 22 hours.

Mutagenesis

114

G → A: Extends the period of the circadian rhythm to 27 hours. Ref.5

Mutagenesis

115

Q → A: Abolishes the circadian rhythm. Ref.5

Mutagenesis

157

S → C in kaiC2; extends the period of the circadian rhythm to 29 hours.

Mutagenesis

215

R → C in kaiC3; shortens the period of the circadian rhythm to 16 hours and decreases the interaction with KaiA.

Mutagenesis

236

P → S in kaiC4; extends the period of the circadian rhythm to 28 hours.

Mutagenesis

248

P → L in kaiC6; induces a low amplitude phenotype and decreases the interaction with KaiA.

Mutagenesis

248

P → S in kaiC5; induces an arrhythmic phenotype.

Mutagenesis

253

R → H in kaiC7; extends the period of the circadian rhythm to 40 hours.

Mutagenesis

273

M → I in kaiC8; extends the period of the circadian rhythm to 37 hours.

Mutagenesis

294

K → A: Induces a long period phenotype. Ref.5

Mutagenesis

321

R → Q in kaiC9; shortens the period of the circadian rhythm to 21 hours.

Mutagenesis

409

T → A in kaiC10; extends the period of the circadian rhythm to 27 hours.

Mutagenesis

421

G → R in kaiC11; extends the period of the circadian rhythm to 44 hours and increases the interaction with KaiA.

Mutagenesis

422

A → T in kaiC15; able to suppress the kaiA2 extended phenotype.

Mutagenesis

432

T → A: Loss of function. Ref.15

Mutagenesis

442

Y → H in kaiC12; extends the period of the circadian rhythm to 60 hours and increases the interaction with KaiA.

Mutagenesis

460

G → E in kaiC13; induces an arrhythmic phenotype.

Mutagenesis

495

T → A in kaiC14; induces an arrhythmic phenotype.

Secondary structure

519

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q79PF4 [UniParc].

Last modified July 5, 2004. Version 1.
Checksum: 855DFE131EFFF3CF
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FASTA

519

58,003

        10         20         30         40         50         60 
MTSAEMTSPN NNSEHQAIAK MRTMIEGFDD ISHGGLPIGR STLVSGTSGT GKTLFSIQFL 

        70         80         90        100        110        120 
YNGIIEFDEP GVFVTFEETP QDIIKNARSF GWDLAKLVDE GKLFILDASP DPEGQEVVGG 

       130        140        150        160        170        180 
FDLSALIERI NYAIQKYRAR RVSIDSVTSV FQQYDASSVV RRELFRLVAR LKQIGATTVM 

       190        200        210        220        230        240 
TTERIEEYGP IARYGVEEFV SDNVVILRNV LEGERRRRTL EILKLRGTSH MKGEYPFTIT 

       250        260        270        280        290        300 
DHGINIFPLG AMRLTQRSSN VRVSSGVVRL DEMCGGGFFK DSIILATGAT GTGKTLLVSR 

       310        320        330        340        350        360 
FVENACANKE RAILFAYEES RAQLLRNAYS WGMDFEEMER QNLLKIVCAY PESAGLEDHL 

       370        380        390        400        410        420 
QIIKSEINDF KPARIAIDSL SALARGVSNN AFRQFVIGVT GYAKQEEITG LFTNTSDQFM 

       430        440        450        460        470        480 
GAHSITDSHI STITDTIILL QYVEIRGEMS RAINVFKMRG SWHDKAIREF MISDKGPDIK 

       490        500        510 
DSFRNFERII SGSPTRITVD EKSELSRIVR GVQEKGPES

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria." Ishiura M., Kutsuna S., Aoki S., Iwasaki H., Andersson C.R., Tanabe A., Golden S.S., Johnson C.H., Kondo T. Science 281:1519-1523(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, MUTANTS KAIC1; KAIC2; KAIC3; KAIC4; KAIC5; KAIC6; KAIC7; KAIC8; KAIC9; KAIC10; KAIC11; KAIC12; KAIC13 AND KAIC14.
[2]	"Synechococcus elongatus PCC7942 cosmid 7G3." Holtman C.K., Sandoval P., Chen Y., Socias T., Mohler B.J., McMurtry S., Gonzalez A., Salinas I., Golden S.S., Youderian P. Submitted (JUN-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Complete sequence of chromosome 1 of Synechococcus elongatus PCC 7942." US DOE Joint Genome Institute Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Schmutz J., Larimer F., Land M., Kyrpides N., Lykidis A., Richardson P. Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: PCC 7942.
[4]	"Physical interactions among circadian clock proteins KaiA, KaiB and KaiC in cyanobacteria." Iwasaki H., Taniguchi Y., Ishiura M., Kondo T. EMBO J. 18:1137-1145(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH KAIA AND KAIB.
[5]	"Nucleotide binding and autophosphorylation of the clock protein KaiC as a circadian timing process of cyanobacteria." Nishiwaki T., Iwasaki H., Ishiura M., Kondo T. Proc. Natl. Acad. Sci. U.S.A. 97:495-499(2000) [PubMed] [Europe PMC] [Abstract] Cited for: ATP-BINDING, AUTOPHOSPHORYLATION, MUTAGENESIS OF LYS-52; GLY-71; GLY-114; GLN-115 AND LYS-294.
[6]	"A kaiC-interacting sensory histidine kinase, SasA, necessary to sustain robust circadian oscillation in cyanobacteria." Iwasaki H., Williams S.B., Kitayama Y., Ishiura M., Golden S.S., Kondo T. Cell 101:223-233(2000) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH SASA.
[7]	"Two KaiA-binding domains of cyanobacterial circadian clock protein KaiC." Taniguchi Y., Yamaguchi A., Hijikata A., Iwasaki H., Kamagata K., Ishiura M., Go M., Kondo T. FEBS Lett. 496:86-90(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH KAIA, MUTANTS KAIC3; KAIC6; KAIC11 AND KAIC12.
[8]	"KaiA-stimulated KaiC phosphorylation in circadian timing loops in cyanobacteria." Iwasaki H., Nishiwaki T., Kitayama Y., Nakajima M., Kondo T. Proc. Natl. Acad. Sci. U.S.A. 99:15788-15793(2002) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION, ENZYME REGULATION, MUTANT KAIC15.
[9]	"Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA." Mori T., Saveliev S.V., Xu Y., Stafford W.F., Cox M.M., Inman R.B., Johnson C.H. Proc. Natl. Acad. Sci. U.S.A. 99:17203-17208(2002) [PubMed] [Europe PMC] [Abstract] Cited for: HEXAMERIZATION, DNA-BINDING, ATP-BINDING.
[10]	"Cyanobacterial circadian clockwork: roles of KaiA, KaiB and the kaiBC promoter in regulating KaiC." Xu Y., Mori T., Johnson C.H. EMBO J. 22:2117-2126(2003) [PubMed] [Europe PMC] [Abstract] Cited for: ENZYME REGULATION, PHOSPHORYLATION, INTERACTION WITH KAIB.
[11]	"KaiB functions as an attenuator of KaiC phosphorylation in the cyanobacterial circadian clock system." Kitayama Y., Iwasaki H., Nishiwaki T., Kondo T. EMBO J. 22:2127-2134(2003) [PubMed] [Europe PMC] [Abstract] Cited for: ENZYME REGULATION, PHOSPHORYLATION, INTERACTION WITH KAIB.
[12]	"Global gene repression by KaiC as a master process of prokaryotic circadian system." Nakahira Y., Katayama M., Miyashita H., Kutsuna S., Iwasaki H., Oyama T., Kondo T. Proc. Natl. Acad. Sci. U.S.A. 101:881-885(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE KAIABC COMPLEX, INDUCTION.
[13]	"Stoichiometric interactions between cyanobacterial clock proteins KaiA and KaiC." Hayashi F., Ito H., Fujita M., Iwase R., Uzumaki T., Ishiura M. Biochem. Biophys. Res. Commun. 316:195-202(2004) [PubMed] [Europe PMC] [Abstract] Cited for: STOICHIOMETRY OF THE COMPLEX FORMED WITH KAIA.
[14]	"Circadian rhythms in the synthesis and degradation of a master clock protein kaiC in cyanobacteria." Imai K., Nishiwaki T., Kondo T., Iwasaki H. J. Biol. Chem. 279:36534-36539(2004) [PubMed] [Europe PMC] [Abstract] Cited for: DEVELOPMENTAL STAGE.
[15]	"Visualizing a circadian clock protein; crystal structure of kaiC and functional insights." Pattanayek R., Wang J., Mori T., Xu Y., Johnson C.H., Egli M. Mol. Cell 15:375-388(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF HEXAMER, COFACTOR, MUTAGENESIS OF THR-432.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB010691 Genomic DNA. Translation: BAA37103.1.
AY120853 Genomic DNA. Translation: AAM82686.1.
CP000100 Genomic DNA. Translation: ABB57246.1.

PIR

T44269.

RefSeq

YP_400233.1. NC_007604.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1TF7	X-ray	2.80	A/B/C/D/E/F	1-519	[»]
1U9I	X-ray	2.80	A/B/C/D/E/F	1-519	[»]
2GBL	X-ray	2.80	A/B/C/D/E/F	1-519	[»]
3DVL	X-ray	2.80	A/B/C/D/E/F	1-519	[»]
3JZM	X-ray	2.90	A/B/C/D/E/F	1-519	[»]
3K09	X-ray	3.20	A/B/C/D/E/F	1-519	[»]
3K0A	X-ray	3.00	A/B/C/D/E/F	1-519	[»]
3K0C	X-ray	3.30	A/B/C/D/E/F	1-519	[»]
3K0E	X-ray	3.20	A/B/C/D/E/F	1-519	[»]
3K0F	X-ray	3.00	A/B/C/D/E/F	1-519	[»]
3S1A	X-ray	3.00	A/B/C/D/E/F	1-519	[»]
4DUG	X-ray	3.30	A/B/C/D/E/F	1-519	[»]
4IJM	X-ray	3.35	A/B/C/D/E/F	14-519	[»]

ProteinModelPortal

Q79PF4.

SMR

Q79PF4. Positions 14-519.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-33330N.

IntAct

Q79PF4. 3 interactions.

STRING

1140.Synpcc7942_1216.

PTM databases

PhosSite

P0501119.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

ABB57246; ABB57246; Synpcc7942_1216.

GeneID

3773504.

KEGG

syf:Synpcc7942_1216.

PATRIC

23787739. VBISynElo51371_1398.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG0467.

HOGENOM

HOG000230416.

K08482.

ProtClustDB

PRK09302.

Enzyme and pathway databases

BioCyc

SELO1140:GJWQ-1238-MONOMER.

Family and domain databases

HAMAP

MF_01836. KaiC.

InterPro

IPR014774. Circ_KaiC/RadA.
IPR013503. Circadian_KaiC.
IPR010624. KaiC_dom.
[Graphical view]

Pfam

PF06745. KaiC. 2 hits.
[Graphical view]

TIGRFAMs

TIGR02655. circ_KaiC. 1 hit.

PROSITE

PS51146. KAIC. 2 hits.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q79PF4.

Entry information

Entry name

KAIC_SYNE7

Accession

Primary (citable) accession number: Q79PF4
Secondary accession number(s): Q31NX3, Q9Z3H2

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	July 5, 2004
Last modified:	May 1, 2013
This is version 85 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents