6YL3 | pdb_00006yl3

High resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
BA [auth 2]	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
EA [auth 5]	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
HA [auth 8]	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
V [auth W]	SCOP2B Superfamily	Urease, gamma-subunit	8078159	3001945	SCOP2B (2022-06-29)
Y [auth Z]	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	e6yl3A1	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)
BA [auth 2]	Urease_gamma	e6yl321	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	e6yl3D1	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)
EA [auth 5]	Urease_gamma	e6yl351	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	e6yl3G1	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)
HA [auth 8]	Urease_gamma	e6yl381	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	e6yl3J1	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)
M	Urease_gamma	e6yl3M1	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)
P	Urease_gamma	e6yl3P1	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)
S	Urease_gamma	e6yl3S1	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)
V [auth W]	Urease_gamma	e6yl3W1	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)
Y [auth Z]	Urease_gamma	e6yl3Z1	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	e6yl3B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
CA [auth 3]	Urease_beta	e6yl331	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	e6yl3E1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
FA [auth 6]	Urease_beta	e6yl361	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	e6yl3H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
IA [auth 9]	Urease_beta	e6yl391	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	e6yl3K1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
N	Urease_beta	e6yl3N1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
Q	Urease_beta	e6yl3Q1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
T	Urease_beta	e6yl3T1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
W [auth X]	Urease_beta	e6yl3X1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
Z [auth 0]	Urease_beta	e6yl301	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Urease, beta-subunit (From Topology)	T: Urease, beta-subunit	F: Urease_beta	ECOD (1.6)
AA [auth 1]	Urease_alpha	e6yl312	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)
AA [auth 1]	Amidohydro_1_N	e6yl311	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
C	Urease_alpha	e6yl3C1	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	e6yl3C2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
DA [auth 4]	Urease_alpha	e6yl341	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)
DA [auth 4]	Amidohydro_1_N	e6yl342	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	e6yl3F2	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	e6yl3F1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
GA [auth 7]	Urease_alpha	e6yl371	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)
GA [auth 7]	Amidohydro_1_N	e6yl372	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	e6yl3I1	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	e6yl3I2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
JA [auth U]	Urease_alpha	e6yl3U1	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)
JA [auth U]	Amidohydro_1_N	e6yl3U2	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	e6yl3L2	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	e6yl3L1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
O	Urease_alpha	e6yl3O2	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)
O	Amidohydro_1_N	e6yl3O1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
R	Urease_alpha	e6yl3R2	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)
R	Amidohydro_1_N	e6yl3R1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
U [auth V]	Urease_alpha	e6yl3V2	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)
U [auth V]	Amidohydro_1_N	e6yl3V1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
X [auth Y]	Urease_alpha	e6yl3Y2	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)
X [auth Y]	Amidohydro_1_N	e6yl3Y1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, BA [auth 2], D, EA [auth 5], G, A, BA [auth 2], D, EA [auth 5], G, HA [auth 8], J, M, P, S, V [auth W], Y [auth Z]	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, CA [auth 3], E, FA [auth 6], H, B, CA [auth 3], E, FA [auth 6], H, IA [auth 9], K, N, Q, T, W [auth X], Z [auth 0]	PF00699	Urease beta subunit (Urease_beta)	Urease beta subunit	This subunit is known as alpha in Heliobacter.	Domain
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	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
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	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, BA [auth 2], D, EA [auth 5], G, A, BA [auth 2], D, EA [auth 5], G, HA [auth 8], J, M, P, S, V [auth W], Y [auth Z]	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 cellular process urea catabolic process amide metabolic process small molecule catabolic process urea metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
B, CA [auth 3], E, FA [auth 6], H, B, CA [auth 3], E, FA [auth 6], H, IA [auth 9], K, N, Q, T, W [auth X], Z [auth 0]	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 cellular process urea catabolic process amide metabolic process small molecule catabolic process urea metabolic process	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex cytoplasm urease complex
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	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 cellular process urea catabolic process amide metabolic process small molecule catabolic process urea metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, BA [auth 2], D, EA [auth 5], G, A, BA [auth 2], D, EA [auth 5], G, HA [auth 8], J, M, P, S, V [auth W], Y [auth Z]	IPR050069	Urease subunit	Family
A, BA [auth 2], D, EA [auth 5], G, A, BA [auth 2], D, EA [auth 5], G, HA [auth 8], J, M, P, S, V [auth W], Y [auth Z]	IPR012010	Urease, gamma subunit	Family
A, BA [auth 2], D, EA [auth 5], G, A, BA [auth 2], D, EA [auth 5], G, HA [auth 8], J, M, P, S, V [auth W], Y [auth Z]	IPR002026	Urease, gamma/gamma-beta subunit	Family
A, BA [auth 2], D, EA [auth 5], G, A, BA [auth 2], D, EA [auth 5], G, HA [auth 8], J, M, P, S, V [auth W], Y [auth Z]	IPR036463	Urease, gamma subunit superfamily	Homologous Superfamily
B, CA [auth 3], E, FA [auth 6], H, B, CA [auth 3], E, FA [auth 6], H, IA [auth 9], K, N, Q, T, W [auth X], Z [auth 0]	IPR002019	Urease, beta subunit-like	Family
B, CA [auth 3], E, FA [auth 6], H, B, CA [auth 3], E, FA [auth 6], H, IA [auth 9], K, N, Q, T, W [auth X], Z [auth 0]	IPR050069	Urease subunit	Family
B, CA [auth 3], E, FA [auth 6], H, B, CA [auth 3], E, FA [auth 6], H, IA [auth 9], K, N, Q, T, W [auth X], Z [auth 0]	IPR036461	Urease, beta subunit superfamily	Homologous Superfamily
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	IPR029754	Urease nickel binding site	Binding Site
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	IPR017950	Urease active site	Active Site
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	IPR006680	Amidohydrolase-related	Domain
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	IPR011059	Metal-dependent hydrolase, composite domain superfamily	Homologous Superfamily
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	IPR032466	Metal-dependent hydrolase	Homologous Superfamily
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	IPR011612	Urease alpha-subunit, N-terminal domain	Domain
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	IPR050112	Urease Alpha Subunit	Family
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	IPR005848	Urease, alpha subunit	Family
AA [auth 1], C, DA [auth 4], F, GA [auth 7], AA [auth 1], C, DA [auth 4], F, GA [auth 7], I, JA [auth U], L, O, R, U [auth V], X [auth Y]	IPR017951	Urease alpha subunit, C-terminal	Domain