5JWR

Crystal structure of foldswitch-stabilized KaiB in complex with the N-terminal CI domain of KaiC and a dimer of KaiA C-terminal domains from Thermosynechococcus elongatus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d5jwrd_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	KaiB-like	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
B	d5jwrb_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	KaiB-like	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8065698	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8065698	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	KaiA/RbsU domain	8041136	3000938	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	KaiA/RbsU domain	8041136	3000938	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	KaiA/RbsU domain	8041136	3000938	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	KaiA/RbsU domain	8041136	3000938	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thioredoxin-like	8084499	3000031	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thioredoxin-like	8084499	3000031	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RecA	e5jwrA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RecA	ECOD (1.6)
C	RecA	e5jwrC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: RecA	ECOD (1.6)
E	KaiA	e5jwrE1	A: alpha arrays	X: KaiA/RbsU domain-like	H: KaiA/RbsU domain (From Topology)	T: KaiA/RbsU domain	F: KaiA	ECOD (1.6)
F	KaiA	e5jwrF1	A: alpha arrays	X: KaiA/RbsU domain-like	H: KaiA/RbsU domain (From Topology)	T: KaiA/RbsU domain	F: KaiA	ECOD (1.6)
H	KaiA	e5jwrH1	A: alpha arrays	X: KaiA/RbsU domain-like	H: KaiA/RbsU domain (From Topology)	T: KaiA/RbsU domain	F: KaiA	ECOD (1.6)
G	KaiA	e5jwrG1	A: alpha arrays	X: KaiA/RbsU domain-like	H: KaiA/RbsU domain (From Topology)	T: KaiA/RbsU domain	F: KaiA	ECOD (1.6)
D	KaiB	e5jwrD1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: KaiB	ECOD (1.6)
B	KaiB	e5jwrB1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: KaiB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF06745	KaiC (ATPase)	KaiC	This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and eukaryotes. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein as ...	This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and eukaryotes. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria [1].	Domain
E, F, G, H	PF07688	KaiA C-terminal domain (KaiA)	KaiA C-terminal domain	The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. The overall fold of the KaiA C-terminal domain is that of a four-helix bundle, which forms a dimer in the known structure [1].	Domain
B, D	PF07689	KaiB domain (KaiB)	KaiB domain	The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. Mutations in both proteins have been reported to alter or abolish circadian rhythmicity. KaiB adopts an alpha-beta meander motif and ...	The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. Mutations in both proteins have been reported to alter or abolish circadian rhythmicity. KaiB adopts an alpha-beta meander motif and is found to be a dimer [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Circadian clock protein kinase KaiC	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding DNA binding nucleic acid binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein serine/threonine/tyrosine kinase activity catalytic activity, acting on a protein protein kinase activity phosphotransferase activity, alcohol group as acceptor protein serine/threonine kinase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides ATP-dependent activity protein serine kinase activity identical protein binding protein binding	rhythmic process circadian rhythm regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process rhythmic process circadian rhythm regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process regulation of circadian rhythm protein phosphorylation organonitrogen compound metabolic process protein autophosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process	-
E, F, G, H	Circadian clock protein KaiA	identical protein binding protein binding binding	rhythmic process circadian rhythm	-
B, D	Circadian clock protein KaiB	-	regulation of biological process regulation of cellular process phosphorylation cellular metabolic process negative regulation of metabolic process biological regulation negative regulation of biological process negative regulation of phosphate metabolic process regulation of cellular metabolic process negative regulation of cellular metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of phosphorus metabolic process negative regulation of cellular process regulation of biological process regulation of cellular process phosphorylation cellular metabolic process negative regulation of metabolic process biological regulation negative regulation of biological process negative regulation of phosphate metabolic process regulation of cellular metabolic process negative regulation of cellular metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of phosphorus metabolic process negative regulation of cellular process regulation of phosphorus metabolic process metabolic process cellular process regulation of phosphorylation negative regulation of phosphorylation phosphorus metabolic process regulation of metabolic process rhythmic process circadian rhythm	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR014774	KaiC-like domain	Domain
A, C	IPR030665	Circadian clock protein kinase KaiC	Family
A, C	IPR047222	Circadian clock protein kinase KaiC, C-terminal domain	Domain
A, C	IPR010624	KaiC domain	Domain
A, C	IPR047221	Circadian clock protein kinase KaiC, N-terminal domain	Domain
A, C	IPR013503	Circadian clock KaiC, bacteria	Family
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
E, F, G, H	IPR011006	CheY-like superfamily	Homologous Superfamily
E, F, G, H	IPR011648	Circadian clock oscillator protein KaiA	Family
E, F, G, H	IPR020844	Circadian clock protein KaiA, N-terminal	Domain
E, F, G, H	IPR017944	KaiA/RbsU helical domain superfamily	Homologous Superfamily
E, F, G, H	IPR020856	Circadian clock oscillator protein KaiA, C-terminal	Domain
B, D	IPR039022	Circadian clock protein KaiB-like	Family
B, D	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
B, D	IPR011649	KaiB domain	Domain
B, D	IPR013474	Circadian clock protein KaiB	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.