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
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)
C	Iso_dh	e6yl3C1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
DA [auth 4]	Iso_dh	e6yl341	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
F	Iso_dh	e6yl3F1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
GA [auth 7]	Iso_dh	e6yl371	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
I	Iso_dh	e6yl3I1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
JA [auth U]	Iso_dh	e6yl3U1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
L	Iso_dh	e6yl3L1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
O	Iso_dh	e6yl3O1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
R	Iso_dh	e6yl3R1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
X [auth Y]	Iso_dh	e6yl3Y1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
U [auth V]	Iso_dh	e6yl3V1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
AA [auth 1]	Iso_dh	e6yl311	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
B	Iso_dh	e6yl3B1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
CA [auth 3]	Iso_dh	e6yl331	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
FA [auth 6]	Iso_dh	e6yl361	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
H	Iso_dh	e6yl3H1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
IA [auth 9]	Iso_dh	e6yl391	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
K	Iso_dh	e6yl3K1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
N	Iso_dh	e6yl3N1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
Q	Iso_dh	e6yl3Q1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
T	Iso_dh	e6yl3T1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
W [auth X]	Iso_dh	e6yl3X1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
Z [auth 0]	Flavi_M	e6yl301	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Flavi_M	ECOD (v294.1)
E	Iso_dh	e6yl3E1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
A	Iso_dh	e6yl3A1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
BA [auth 2]	Iso_dh	e6yl321	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
D	Iso_dh	e6yl3D1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
EA [auth 5]	Iso_dh	e6yl351	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
G	Iso_dh	e6yl3G1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
HA [auth 8]	Iso_dh	e6yl381	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
J	Iso_dh	e6yl3J1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
M	Iso_dh	e6yl3M1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
P	Iso_dh	e6yl3P1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
S	Iso_dh	e6yl3S1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
V [auth W]	Iso_dh	e6yl3W1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)
Y [auth Z]	Iso_dh	e6yl3Z1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Iso_dh	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 small molecule metabolic process metabolic process cellular process urea catabolic 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 small molecule metabolic process metabolic process cellular process urea catabolic process small molecule catabolic process urea metabolic process	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex cytoplasm urease complex
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 small molecule metabolic process metabolic process cellular process urea catabolic 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
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
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
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