4G86

Crystal structure of the redox-active cofactor DBMIB bound to the full length circadian clock protein KaiA from Synechococcus elongatus

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	CheY-like	8038789	3001156	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	KaiA/RbsU domain	8038787	3000938	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CheY-like	8038789	3001156	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	KaiA/RbsU domain	8038787	3000938	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	PF07688	e4g86A1	A: alpha arrays	X: KaiA/RbsU domain-like	H: KaiA/RbsU domain (From Topology)	T: KaiA/RbsU domain	F: PF07688	ECOD (1.6)
A	PF21714	e4g86A2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: PF21714	ECOD (1.6)
B	PF07688	e4g86B3	A: alpha arrays	X: KaiA/RbsU domain-like	H: KaiA/RbsU domain (From Topology)	T: KaiA/RbsU domain	F: PF07688	ECOD (1.6)
B	PF21714	e4g86B2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: PF21714	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
A	1.10.1240.30	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	1.10.1240.30	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21714	Circadian clock protein KaiA, N-terminal domain (KaiA_N)	Circadian clock protein KaiA, N-terminal domain	This domain is found at the N-terminal end of Circadian clock protein KaiA from Synechococcus elongatus and similar bacterial proteins. KaiA is essential for circadian timekeeping. This protein organised into two domains. This entry represents the a ...	This domain is found at the N-terminal end of Circadian clock protein KaiA from Synechococcus elongatus and similar bacterial proteins. KaiA is essential for circadian timekeeping. This protein organised into two domains. This entry represents the a pseudo-receiver domain, which has a similar fold with that of bacterial response regulators, with an alpha-beta structure [1-5].	Domain
A, B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Circadian clock protein kaiA	identical protein binding protein binding binding	negative regulation of protein dephosphorylation protein dephosphorylation regulation of cellular process regulation of protein modification process negative regulation of biological process negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process organic substance metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of cellular process negative regulation of protein modification process negative regulation of dephosphorylation negative regulation of protein dephosphorylation protein dephosphorylation regulation of cellular process regulation of protein modification process negative regulation of biological process negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process organic substance metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of cellular process negative regulation of protein modification process negative regulation of dephosphorylation protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process organonitrogen compound metabolic process regulation of dephosphorylation regulation of protein dephosphorylation dephosphorylation cellular metabolic process negative regulation of metabolic process regulation of protein metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process macromolecule modification negative regulation of phosphorus metabolic process metabolic process cellular process regulation of phosphorus metabolic process macromolecule metabolic process regulation of metabolic process rhythmic process circadian rhythm positive regulation of circadian rhythm positive regulation of biological process regulation of circadian rhythm detection of stimulus response to stimulus response to chemical detection of redox state detection of chemical stimulus response to redox state entrainment of circadian clock response to external stimulus	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011006	CheY-like superfamily	Homologous Superfamily
A, B	IPR011648	Circadian clock oscillator protein KaiA	Family
A, B	IPR020844	Circadian clock protein KaiA, N-terminal	Domain
A, B	IPR017944	KaiA/RbsU helical domain superfamily	Homologous Superfamily
A, B	IPR020856	Circadian clock oscillator protein KaiA, C-terminal	Domain

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.