3QGA | pdb_00003qga

3.0 A Model of Iron Containing Urease UreA2B2 from Helicobacter mustelae

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
K [auth P]	FeoB_Cyto	e3qgaP1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FeoB_Cyto	ECOD (v294.1)
I [auth M]	FeoB_Cyto	e3qgaM1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FeoB_Cyto	ECOD (v294.1)
G [auth J]	FeoB_Cyto	e3qgaJ1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FeoB_Cyto	ECOD (v294.1)
E [auth G]	FeoB_Cyto	e3qgaG1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FeoB_Cyto	ECOD (v294.1)
C [auth D]	FeoB_Cyto	e3qgaD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FeoB_Cyto	ECOD (v294.1)
A	Fis1_TPR_N,Fis1_TPR_C	e3qgaA1	A: a/b three-layered sandwiches	X: Cystatin-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Fis1_TPR_N,Fis1_TPR_C	ECOD (v294.1)
L [auth R]		e3qgaR3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (v294.1)
J [auth O]		e3qgaO3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (v294.1)
H [auth L]		e3qgaL3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (v294.1)
F [auth I]		e3qgaI3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (v294.1)
D [auth F]		e3qgaF3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (v294.1)
B [auth C]		e3qgaC3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K [auth P]	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (4.3.0)
K [auth P]	2.10.150.10	Mainly Beta	Ribbon	Urease, subunit B	Urease, beta subunit	CATH (4.3.0)
I [auth M]	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (4.3.0)
I [auth M]	2.10.150.10	Mainly Beta	Ribbon	Urease, subunit B	Urease, beta subunit	CATH (4.3.0)
G [auth J]	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (4.3.0)
G [auth J]	2.10.150.10	Mainly Beta	Ribbon	Urease, subunit B	Urease, beta subunit	CATH (4.3.0)
E [auth G]	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (4.3.0)
E [auth G]	2.10.150.10	Mainly Beta	Ribbon	Urease, subunit B	Urease, beta subunit	CATH (4.3.0)
C [auth D]	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (4.3.0)
C [auth D]	2.10.150.10	Mainly Beta	Ribbon	Urease, subunit B	Urease, beta subunit	CATH (4.3.0)
A	3.30.280.10	Alpha Beta	2-Layer Sandwich	Urease	subunit A	CATH (4.3.0)
A	2.10.150.10	Mainly Beta	Ribbon	Urease, subunit B	Urease, beta subunit	CATH (4.3.0)
L [auth R]	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
L [auth R]	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
J [auth O]	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
J [auth O]	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
H [auth L]	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
H [auth L]	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
F [auth I]	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
F [auth I]	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
D [auth F]	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
D [auth F]	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
B [auth C]	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
B [auth C]	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, C [auth D], E [auth G], G [auth J], I [auth M], A, C [auth D], E [auth G], G [auth J], I [auth M], K [auth P]	PF00699	Urease beta subunit (Urease_beta)	Urease beta subunit	This subunit is known as alpha in Heliobacter.	Domain
A, C [auth D], E [auth G], G [auth J], I [auth M], A, C [auth D], E [auth G], G [auth J], I [auth M], K [auth P]	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 [auth C], D [auth F], F [auth I], H [auth L], J [auth O], B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], L [auth R]	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
B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], L [auth R]	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, C [auth D], E [auth G], G [auth J], I [auth M], A, C [auth D], E [auth G], G [auth J], I [auth M], K [auth P]	Fusion of urease beta and gamma subunits	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 identical protein binding protein 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	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex cytoplasm urease complex
B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], L [auth R]	Urease subunit beta 2	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
A, C [auth D], E [auth G], G [auth J], I [auth M], A, C [auth D], E [auth G], G [auth J], I [auth M], K [auth P]	IPR002019	Urease, beta subunit-like	Family
A, C [auth D], E [auth G], G [auth J], I [auth M], A, C [auth D], E [auth G], G [auth J], I [auth M], K [auth P]	IPR050069	Urease subunit	Family
A, C [auth D], E [auth G], G [auth J], I [auth M], A, C [auth D], E [auth G], G [auth J], I [auth M], K [auth P]	IPR008223	Urease, gamma-beta subunit	Family
A, C [auth D], E [auth G], G [auth J], I [auth M], A, C [auth D], E [auth G], G [auth J], I [auth M], K [auth P]	IPR036461	Urease, beta subunit superfamily	Homologous Superfamily
A, C [auth D], E [auth G], G [auth J], I [auth M], A, C [auth D], E [auth G], G [auth J], I [auth M], K [auth P]	IPR002026	Urease, gamma/gamma-beta subunit	Family
A, C [auth D], E [auth G], G [auth J], I [auth M], A, C [auth D], E [auth G], G [auth J], I [auth M], K [auth P]	IPR036463	Urease, gamma subunit superfamily	Homologous Superfamily
B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], L [auth R]	IPR011612	Urease alpha-subunit, N-terminal domain	Domain
B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], L [auth R]	IPR050112	Urease Alpha Subunit	Family
B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], L [auth R]	IPR005848	Urease, alpha subunit	Family
B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], L [auth R]	IPR006680	Amidohydrolase-related	Domain
B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], L [auth R]	IPR011059	Metal-dependent hydrolase, composite domain superfamily	Homologous Superfamily
B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], L [auth R]	IPR032466	Metal-dependent hydrolase	Homologous Superfamily
B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], L [auth R]	IPR017951	Urease alpha subunit, C-terminal	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C [auth D], E [auth G], G [auth J], I [auth M], A, C [auth D], E [auth G], G [auth J], I [auth M], K [auth P]	FME	Parent Component: MET RESID: AA0021 , AA0566 PSI-MOD : N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891
B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], B [auth C], D [auth F], F [auth I], H [auth L], J [auth O], L [auth R]	KCX	Parent Component: LYS RESID: AA0021 , AA0566