Circadian clock protein KaiA - Synechococcus elongatus (strain PCC 7942)

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Q79PF6 (KAIA_SYNE7) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 68. 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 KaiA

Gene names

Name:	kaiA
Ordered Locus Names:	Synpcc7942_1218
ORF Names:	see0009

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	284 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. The KaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction. In the complex, it enhances the phosphorylation status of KaiC. In contrast, the presence of KaiB in the complex decreases the phosphorylation status of KaiC, suggesting that KaiB acts by antagonizing the interaction between KaiA and KaiC. A KaiA dimer is sufficient to enhance KaiC hexamer phosphorylation. Ref.1 Ref.7 Ref.8 Ref.9
Subunit structure	Homodimer. Component of the KaiABC complex, at least composed of a KaiC homohexamer, a KaiB dimer and two KaiA dimers. The KaiABC complex also interacts with SasA. Ref.4 Ref.5 Ref.13
Developmental stage	Expressed constantly throughout the circadian cycle. Ref.9
Domain	The N-terminal part (1-102), which is also called pseudo-receiver domain, does not enhance KaiC autophosphorylation. It may have an amplitude-amplifier function and may be involved in transducing input signals to the KaiABC complex. This domain is not conserved in other species. Ref.13 The KaiA domain mediates the interaction with KaiC, the homodimerization, and is responsible for the clock oscillation function. Ref.13
Miscellaneous	'Kai' means 'cycle' in Japanese.
Sequence similarities	Contains 1 kaiA C-terminal domain. Contains 1 kaiA N-terminal domain.
Caution	Ref.13 structure is derived from this sequence and not from the one of S.elongatus.

Ontologies

Keywords
Biological process	Biological rhythms
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological_process	circadian rhythm Inferred from electronic annotation. Source: InterPro entrainment of circadian clock Inferred from direct assay Ref.4. Source: UniProtKB positive regulation of circadian rhythm Inferred from direct assay Ref.5. Source: UniProtKB protein phosphorylation Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct
itself		2	EBI-592281,EBI-592281
kaiB	Q79PF5	9	EBI-592281,EBI-619150
kaiC	Q79PF4	17	EBI-592281,EBI-592287
ldpA	Q8GLI4	2	EBI-592281,EBI-626836

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 284

284

Circadian clock protein KaiA

PRO_0000217871

Regions

Domain

1 – 164

164

KaiA N-terminal

Domain

174 – 282

109

KaiA C-terminal

Experimental info

Mutagenesis

I → T: Extends the period of the circadian rhythm to 29 hours. Ref.6

Mutagenesis

I → F: Extends the period of the circadian rhythm to 27 hours. Ref.6

Mutagenesis

L → P: Extends the period of the circadian rhythm to 27 hours. Ref.6

Mutagenesis

S → P: Extends the period of the circadian rhythm to 29 hours. Ref.6

Mutagenesis

C → S: Induces an arrhythmic phenotype. Ref.6

Mutagenesis

V → G: Extends the period of the circadian rhythm to 28 hours. Ref.6

Mutagenesis

103

E → K in kaiA1; extends the period of the circadian rhythm to 33 hours and increases the interaction with KaiB.

Mutagenesis

113

Q → R: Extends the period of the circadian rhythm to 33 hours. Ref.6

Mutagenesis

117

Q → L: Extends the period of the circadian rhythm to 26 hours. Ref.6

Mutagenesis

119

D → E: Extends the period of the circadian rhythm to 30 hours. Ref.6

Mutagenesis

119

D → G: Extends the period of the circadian rhythm to 26 hours. Ref.6

Mutagenesis

131

V → A: Extends the period of the circadian rhythm to 28 hours. Ref.6

Mutagenesis

136

D → V: Extends the period of the circadian rhythm to 30 hours. Ref.6

Mutagenesis

136

D → Y: Extends the period of the circadian rhythm to 29 hours. Ref.6

Mutagenesis

166

Y → C in kaiA3; induces an arrhythmic phenotype and reduces the interaction with KaiC.

Mutagenesis

178

F → S or I: Induces an arrhythmic phenotype. Ref.6

Mutagenesis

180

R → H: Extends the period of the circadian rhythm to 26 hours. Ref.6

Mutagenesis

194

M → T: Extends the period of the circadian rhythm to 26 hours. Ref.6

Mutagenesis

224

F → S: Induces an arrhythmic phenotype. Ref.6

Mutagenesis

225

F → S: Induces an arrhythmic phenotype. Ref.6

Mutagenesis

239

E → G: Extends the period of the circadian rhythm to 28 hours. Ref.6

Mutagenesis

241

M → T: Extends the period of the circadian rhythm to 38 hours. Ref.6

Mutagenesis

242

D → V or G: Extends the period of the circadian rhythm to 27 hours. Ref.6

Mutagenesis

243

E → A: Extends the period of the circadian rhythm to 34 hours. Ref.6

Mutagenesis

244

F → V: Extends the period of the circadian rhythm to 26 hours. Ref.6

Mutagenesis

245

A → D: Extends the period of the circadian rhythm to 26 hours. Ref.6

Mutagenesis

249

R → H in kaiA1; extends the period of the circadian rhythm to 30 hours.

Mutagenesis

266

I → V: Extends the period of the circadian rhythm to 27 hours. Ref.6

Mutagenesis

273

C → Y: Extends the period of the circadian rhythm to 30 hours. Ref.6

Mutagenesis

274

E → K in kaiA3; induces an arrhythmic phenotype.

Secondary structure

284

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q79PF6 [UniParc].

Last modified July 5, 2004. Version 1.
Checksum: 7C4F3B79FFDF59A2
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FASTA

284

32,632

        10         20         30         40         50         60 
MLSQIAICIW VESTAILQDC QRALSADRYQ LQVCESGEML LEYAQTHRDQ IDCLILVAAN 

        70         80         90        100        110        120 
PSFRAVVQQL CFEGVVVPAI VVGDRDSEDP DEPAKEQLYH SAELHLGIHQ LEQLPYQVDA 

       130        140        150        160        170        180 
ALAEFLRLAP VETMADHIML MGANHDPELS SQQRDLAQRL QERLGYLGVY YKRDPDRFLR 

       190        200        210        220        230        240 
NLPAYESQKL HQAMQTSYRE IVLSYFSPNS NLNQSIDNFV NMAFFADVPV TKVVEIHMEL 

       250        260        270        280 
MDEFAKKLRV EGRSEDILLD YRLTLIDVIA HLCEMYRRSI PRET

« 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 KAIA1; KAIA2 AND KAIA3.
[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 KAIC AND KAIB, MUTANT KAIA1.
[5]	"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 KAIC, MUTANTS KAIA2 AND KAIA4.
[6]	"Mutations in KaiA, a clock protein, extend the period of circadian rhythm in the cyanobacterium Synechococcus elongatus PCC 7942." Nishimura H., Nakahira Y., Imai K., Tsuruhara A., Kondo H., Hayashi H., Hirai M., Saito H., Kondo T. Microbiology 148:2903-2909(2002) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ILE-9; ILE-16; LEU-31; SER-36; CYS-53; VAL-76; GLN-113; GLN-117; ASP-119; VAL-131; ASP-136; PHE-178; ARG-180; MET-194; PHE-224; PHE-225; GLU-239; MET-241; ASP-242; GLU-243; PHE-244; ALA-245; ILE-266 AND CYS-273.
[7]	"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: FUNCTION.
[8]	"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: FUNCTION.
[9]	"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: FUNCTION, DEVELOPMENTAL STAGE.
[10]	"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 KAIC.
[11]	"Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism." Williams S.B., Vakonakis I., Golden S.S., LiWang A.C. Proc. Natl. Acad. Sci. U.S.A. 99:15357-15362(2002) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 1-135.
[12]	Erratum Williams S.B., Vakonakis I., Golden S.S., LiWang A.C. Proc. Natl. Acad. Sci. U.S.A. 100:763-763(2003)
[13]	"Crystal structure of circadian clock protein KaiA from Synechococcus elongatus." Ye S., Vakonakis I., Ioerger T.R., LiWang A.C., Sacchettini J.C. J. Biol. Chem. 279:20511-20518(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.03 ANGSTROMS) OF 2-284, HOMODIMERIZATION, DOMAIN.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB010691 Genomic DNA. Translation: BAA37101.1.
AY120853 Genomic DNA. Translation: AAM82684.1.
CP000100 Genomic DNA. Translation: ABB57248.1.

PIR

T44267.

RefSeq

YP_400235.1. NC_007604.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1M2E	NMR	-	A	1-135	[»]
1M2F	NMR	-	A	1-135	[»]
1R8J	X-ray	2.03	A/B	2-284	[»]
4G86	X-ray	2.39	A/B	2-284	[»]

ProteinModelPortal

Q79PF6.

SMR

Q79PF6. Positions 1-282.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-33329N.

IntAct

Q79PF6. 4 interactions.

STRING

1140.Synpcc7942_1218.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

ABB57248; ABB57248; Synpcc7942_1218.

GeneID

3773506.

KEGG

syf:Synpcc7942_1218.

PATRIC

23787743. VBISynElo51371_1400.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

NOG123092.

HOGENOM

HOG000276784.

K08480.

ProtClustDB

CLSK893788.

Enzyme and pathway databases

BioCyc

SELO1140:GJWQ-1240-MONOMER.

Family and domain databases

Gene3D

1.10.1240.30. 1 hit.

InterPro

IPR011006. CheY-like_superfamily.
IPR011648. Circadian_clock_KaiA.
IPR020844. Circadian_clock_KaiA_N.
IPR020856. Circadian_clock_protein_KaiA_C.
IPR017944. KaiA/RbsU_helical_domain.
[Graphical view]

Pfam

PF07688. KaiA. 1 hit.
[Graphical view]

SUPFAM

SSF52172. CheY_like. 1 hit.
SSF101215. KaiA/RbsU_helical_dom. 1 hit.

PROSITE

PS51431. KAIA_C. 1 hit.
PS51430. KAIA_N. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q79PF6.

Entry information

Entry name

KAIA_SYNE7

Accession

Primary (citable) accession number: Q79PF6
Secondary accession number(s): Q31NX1, Q9Z3H4

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	July 5, 2004
Last modified:	May 1, 2013
This is version 68 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

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction 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