Annotations: 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
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e 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	IRS	e2w27B1	A: beta barrels	X: HTH	H: Nudix	T: Nudix	F: IRS	ECOD (v294.2)
A	Pyr_redox_2	e2w27A1	A: beta barrels	X: UBC-like	H: UBC-like	T: Concanavalin A-like lectins/glucanases	F: Pyr_redox_2	ECOD (v294.2)

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 that ...	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	YKUI PROTEIN	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity cyclic-guanylate-specific phosphodiesterase activity hydrolase activity catalytic activity	-	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018842	YkuI, C-terminal	Domain
A, B	IPR050706	Cyclic-di-GMP_PDE-like	Unknown
A, B	IPR029151	Periplasmic sensor-like domain superfamily	Homologous Superfamily
A, B	IPR001633	EAL domain	Domain
A, B	IPR035919	EAL domain superfamily	Homologous Superfamily

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.