5Z19

The crystal structure of Ruminococcus gnavus beta-glucuronidase in complex with uronic isofagomine

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d5z19a2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
A	d5z19a1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
A	d5z19a3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
B	d5z19b2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
B	d5z19b1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
B	d5z19b3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
E	d5z19e2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
E	d5z19e1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
E	d5z19e3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
C	d5z19c2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
C	d5z19c1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
C	d5z19c3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
D	d5z19d2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
D	d5z19d1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
D	d5z19d3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
F	d5z19f2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
F	d5z19f1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)
F	d5z19f3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Mediterraneibacter gnavus ) [TaxId: 33038 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Glyco_hydro_2_N	e5z19A1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Glyco_hydro_2_N	ECOD (1.6)
A	Glyco_hydro_2	e5z19A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_2	ECOD (1.6)
A	Glyco_hydro_2_C	e5z19A3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_2_C	ECOD (1.6)
B	Glyco_hydro_2_N	e5z19B1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Glyco_hydro_2_N	ECOD (1.6)
B	Glyco_hydro_2	e5z19B3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_2	ECOD (1.6)
B	Glyco_hydro_2_C	e5z19B2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_2_C	ECOD (1.6)
E	Glyco_hydro_2_N	e5z19E2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Glyco_hydro_2_N	ECOD (1.6)
E	Glyco_hydro_2	e5z19E3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_2	ECOD (1.6)
E	Glyco_hydro_2_C	e5z19E1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_2_C	ECOD (1.6)
C	Glyco_hydro_2_N	e5z19C2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Glyco_hydro_2_N	ECOD (1.6)
C	Glyco_hydro_2	e5z19C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_2	ECOD (1.6)
C	Glyco_hydro_2_C	e5z19C3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_2_C	ECOD (1.6)
D	Glyco_hydro_2_N	e5z19D3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Glyco_hydro_2_N	ECOD (1.6)
D	Glyco_hydro_2	e5z19D2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_2	ECOD (1.6)
D	Glyco_hydro_2_C	e5z19D1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_2_C	ECOD (1.6)
F	Glyco_hydro_2_N	e5z19F3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Glyco_hydro_2_N	ECOD (1.6)
F	Glyco_hydro_2	e5z19F2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_2	ECOD (1.6)
F	Glyco_hydro_2_C	e5z19F1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_2_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (utative)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (utative)
B	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (utative)
E	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (utative)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (utative)
C	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (utative)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (utative)
D	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (utative)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (utative)
F	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (utative)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
F	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02836	Glycosyl hydrolases family 2, TIM barrel domain (Glyco_hydro_2_C)	Glycosyl hydrolases family 2, TIM barrel domain	This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.	Domain
A, B, C, D, E A, B, C, D, E, F	PF00703	Glycosyl hydrolases family 2 (Glyco_hydro_2)	Glycosyl hydrolases family 2	This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.	Domain
A, B, C, D, E A, B, C, D, E, F	PF02837	Glycosyl hydrolases family 2, sugar binding domain (Glyco_hydro_2_N)	Glycosyl hydrolases family 2, sugar binding domain	This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold. The domain binds the sugar moiety during the sugar-hydrolysis reaction.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Beta-glucuronidase	binding carbohydrate binding hydrolase activity, acting on glycosyl bonds beta-galactosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity galactosidase activity beta-glucuronidase activity	carbohydrate metabolic process primary metabolic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006101	Glycoside hydrolase, family 2	Family
A, B, C, D, E A, B, C, D, E, F	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006102	Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036156	Beta-Galactosidase/glucuronidase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006104	Glycosyl hydrolases family 2, sugar binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006103	Glycoside hydrolase family 2, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR023230	Glycoside hydrolase, family 2, conserved site	Conserved Site

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.