2W27

CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS YKUI PROTEIN, WITH AN EAL DOMAIN, IN COMPLEX WITH SUBSTRATE C-DI-GMP AND CALCIUM

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family 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)
B	d2w27b1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	EAL domain-like	EAL domain	Hypothetical protein YkuI, N-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2w27b2	Alpha and beta proteins (a+b)	Profilin-like	Sensory domain-like	YkuI C-terminal domain-like	Hypothetical protein YkuI, C-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d2w27a1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	EAL domain-like	EAL domain	Hypothetical protein YkuI, N-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d2w27a2	Alpha and beta proteins (a+b)	Profilin-like	Sensory domain-like	YkuI C-terminal domain-like	Hypothetical protein YkuI, C-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Sensory domain-like	8037827	3001802	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EAL domain-like	8037826	3001190	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EAL domain-like	8037826	3001190	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sensory domain-like	8037827	3001802	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)
B	YkuI_C	e2w27B1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: YkuI_C	ECOD (1.6)
B	EAL	e2w27B2	A: a/b barrels	X: TIM beta/alpha-barrel	H: EAL domain (From Topology)	T: EAL domain	F: EAL	ECOD (1.6)
A	YkuI_C	e2w27A1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: YkuI_C	ECOD (1.6)
A	EAL	e2w27A2	A: a/b barrels	X: TIM beta/alpha-barrel	H: EAL domain (From Topology)	T: EAL domain	F: EAL	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.20.450	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	EAL domain	CATH (4.3.0)
B	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
A	3.20.20.450	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	EAL domain	CATH (4.3.0)
A	1.20.5.170	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF10388	EAL-domain associated signalling protein domain (YkuI_C)	EAL-domain associated signalling protein domain	In Bacillus species this highly conserved region of the YkuI protein lies immediately downstream of the EAL (diguanylate cyclase/phosphodiesterase domain 2) Pfam:PF00563 domain so that together they form a monomer which dimerises for its enzymatic ac ...	In Bacillus species this highly conserved region of the YkuI protein lies immediately downstream of the EAL (diguanylate cyclase/phosphodiesterase domain 2) Pfam:PF00563 domain so that together they form a monomer which dimerises for its enzymatic action. The region contains three alpha helices and five beta strands and is the C-terminal half of the structure.	Domain
A, B	PF00563	EAL domain (EAL)	EAL domain	This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function [1]. The domain contains many conserved acidic residues tha ...	This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function [1]. The domain contains many conserved acidic residues that could participate in metal binding and might form the phosphodiesterase active site [1].	Domain

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018842	YkuI, C-terminal	Domain
A, B	IPR029151	Periplasmic sensor-like domain superfamily	Homologous Superfamily
A, B	IPR001633	EAL domain	Domain
A, B	IPR035919	EAL domain superfamily	Homologous Superfamily

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.