4Z42

Crystal structure of urease from Yersinia enterocolitica

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)
A	d4z42a_	Alpha and beta proteins (a+b)	Urease, gamma-subunit	Urease, gamma-subunit	automated matches	automated matches	(Yersinia enterocolitica W22703 ) [TaxId: 913028 ],	SCOPe (2.08)
D	d4z42d_	Alpha and beta proteins (a+b)	Urease, gamma-subunit	Urease, gamma-subunit	automated matches	automated matches	(Yersinia enterocolitica W22703 ) [TaxId: 913028 ],	SCOPe (2.08)
G	d4z42g_	Alpha and beta proteins (a+b)	Urease, gamma-subunit	Urease, gamma-subunit	automated matches	automated matches	(Yersinia enterocolitica W22703 ) [TaxId: 913028 ],	SCOPe (2.08)
J	d4z42j_	Alpha and beta proteins (a+b)	Urease, gamma-subunit	Urease, gamma-subunit	automated matches	automated matches	(Yersinia enterocolitica W22703 ) [TaxId: 913028 ],	SCOPe (2.08)
B	d4z42b_	All beta proteins	beta-clip	Urease, beta-subunit	automated matches	automated matches	(Yersinia enterocolitica W22703 ) [TaxId: 913028 ],	SCOPe (2.08)
E	d4z42e_	All beta proteins	beta-clip	Urease, beta-subunit	automated matches	automated matches	(Yersinia enterocolitica W22703 ) [TaxId: 913028 ],	SCOPe (2.08)
H	d4z42h_	All beta proteins	beta-clip	Urease, beta-subunit	automated matches	automated matches	(Yersinia enterocolitica W22703 ) [TaxId: 913028 ],	SCOPe (2.08)
K	d4z42k_	All beta proteins	beta-clip	Urease, beta-subunit	automated matches	automated matches	(Yersinia enterocolitica W22703 ) [TaxId: 913028 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Urease, gamma-subunit	8078158	4000909	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	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	Urease_gamma	e4z42A1	A: a+b two layers	X: Urease, gamma-subunit (From Topology)	H: Urease, gamma-subunit (From Topology)	T: Urease, gamma-subunit	F: Urease_gamma	ECOD (1.6)
D	Urease_gamma	e4z42D1	A: a+b two layers	X: Urease, gamma-subunit (From Topology)	H: Urease, gamma-subunit (From Topology)	T: Urease, gamma-subunit	F: Urease_gamma	ECOD (1.6)
G	Urease_gamma	e4z42G1	A: a+b two layers	X: Urease, gamma-subunit (From Topology)	H: Urease, gamma-subunit (From Topology)	T: Urease, gamma-subunit	F: Urease_gamma	ECOD (1.6)
J	Urease_gamma	e4z42J1	A: a+b two layers	X: Urease, gamma-subunit (From Topology)	H: Urease, gamma-subunit (From Topology)	T: Urease, gamma-subunit	F: Urease_gamma	ECOD (1.6)
B	Urease_beta	e4z42B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
E	Urease_beta	e4z42E1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
H	Urease_beta	e4z42H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
K	Urease_beta	e4z42K1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
C	Urease_alpha	e4z42C1	A: beta sandwiches	X: Composite domain of metallo-dependent hydrolases (From Topology)	H: Composite domain of metallo-dependent hydrolases (From Topology)	T: Composite domain of metallo-dependent hydrolases	F: Urease_alpha	ECOD (1.6)
C	Amidohydro_1_N	e4z42C2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
F	Urease_alpha	e4z42F1	A: beta sandwiches	X: Composite domain of metallo-dependent hydrolases (From Topology)	H: Composite domain of metallo-dependent hydrolases (From Topology)	T: Composite domain of metallo-dependent hydrolases	F: Urease_alpha	ECOD (1.6)
F	Amidohydro_1_N	e4z42F2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
I	Urease_alpha	e4z42I1	A: beta sandwiches	X: Composite domain of metallo-dependent hydrolases (From Topology)	H: Composite domain of metallo-dependent hydrolases (From Topology)	T: Composite domain of metallo-dependent hydrolases	F: Urease_alpha	ECOD (1.6)
I	Amidohydro_1_N	e4z42I2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
L	Urease_alpha	e4z42L2	A: beta sandwiches	X: Composite domain of metallo-dependent hydrolases (From Topology)	H: Composite domain of metallo-dependent hydrolases (From Topology)	T: Composite domain of metallo-dependent hydrolases	F: Urease_alpha	ECOD (1.6)
L	Amidohydro_1_N	e4z42L1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (4.3.0)
D	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (4.3.0)
G	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (4.3.0)
J	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (4.3.0)
B	2.10.150.10	Mainly Beta	Ribbon	Urease, subunit B	Urease, beta subunit	CATH (4.3.0)
E	2.10.150.10	Mainly Beta	Ribbon	Urease, subunit B	Urease, beta subunit	CATH (4.3.0)
H	2.10.150.10	Mainly Beta	Ribbon	Urease, subunit B	Urease, beta subunit	CATH (4.3.0)
K	2.10.150.10	Mainly Beta	Ribbon	Urease, subunit B	Urease, beta subunit	CATH (4.3.0)
C	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
C	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
F	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
F	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
I	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
I	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
L	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
L	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J	PF00547	Urease, gamma subunit (Urease_gamma)	Urease, gamma subunit	Urease is a nickel-binding enzyme that catalyses the hydrolysis of urea to carbon dioxide and ammonia.	Domain
B, E, H, K	PF00699	Urease beta subunit (Urease_beta)	Urease beta subunit	This subunit is known as alpha in Heliobacter.	Domain
C, F, I, L	PF00449	Urease alpha-subunit, N-terminal domain (Urease_alpha)	Urease alpha-subunit, N-terminal domain	The N-terminal domain is a composite domain and plays a major trimer stabilising role by contacting the catalytic domain of the symmetry related alpha-subunit.	Domain
C, F, I, L	PF01979	Amidohydrolase family (Amidohydro_1)	Amidohydrolase family	This family of enzymes are a a large metal dependent hydrolase superfamily [1]. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisatio ...	This family of enzymes are a a large metal dependent hydrolase superfamily [1]. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source [2]. This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyse the reaction N-acetyl-D-glucosamine 6-phosphate + H2O <=> D-glucosamine 6-phosphate + acetate. This family includes the catalytic domain of urease alpha subunit [3]. Dihydroorotases (EC:3.5.2.3) are also included [4-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G, J	Urease subunit gamma	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity urease activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding	nitrogen cycle metabolic process catabolic process amide catabolic process small molecule metabolic process metabolic process urea catabolic process amide metabolic process small molecule catabolic process urea metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity
B, E, H, K	Urease subunit beta	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity urease activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	nitrogen cycle metabolic process catabolic process amide catabolic process small molecule metabolic process metabolic process urea catabolic process amide metabolic process small molecule catabolic process urea metabolic process	protein-containing complex intracellular anatomical structure catalytic complex cytoplasm cellular anatomical entity urease complex
C, F, I, L	Urease subunit alpha	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity urease activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding	nitrogen cycle metabolic process catabolic process amide catabolic process small molecule metabolic process metabolic process urea catabolic process amide metabolic process small molecule catabolic process urea metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G, J	IPR050069	Urease subunit	Family
A, D, G, J	IPR012010	Urease, gamma subunit	Family
A, D, G, J	IPR002026	Urease, gamma/gamma-beta subunit	Family
A, D, G, J	IPR036463	Urease, gamma subunit superfamily	Homologous Superfamily
B, E, H, K	IPR002019	Urease, beta subunit-like	Family
B, E, H, K	IPR050069	Urease subunit	Family
B, E, H, K	IPR036461	Urease, beta subunit superfamily	Homologous Superfamily
C, F, I, L	IPR029754	Urease nickel binding site	Binding Site
C, F, I, L	IPR017950	Urease active site	Active Site
C, F, I, L	IPR006680	Amidohydrolase-related	Domain
C, F, I, L	IPR011059	Metal-dependent hydrolase, composite domain superfamily	Homologous Superfamily
C, F, I, L	IPR032466	Metal-dependent hydrolase	Homologous Superfamily
C, F, I, L	IPR011612	Urease alpha-subunit, N-terminal domain	Domain
C, F, I, L	IPR050112	Urease Alpha Subunit	Family
C, F, I, L	IPR005848	Urease, alpha subunit	Family
C, F, I, L	IPR017951	Urease alpha subunit, C-terminal	Domain

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 R01GM133198.