2V5C

Family 84 glycoside hydrolase from Clostridium perfringens, 2.1 Angstrom structure

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	d2v5ca3	All alpha proteins	Hyaluronidase domain-like	Hyaluronidase post-catalytic domain-like	Hyaluronidase post-catalytic domain-like	Hyaluronidase, post-catalytic domain 3	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
A	d2v5ca2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	alpha-D-glucuronidase/Hyaluronidase catalytic domain	Hyaluronidase catalytic domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
A	d2v5ca1	Alpha and beta proteins (a+b)	Zincin-like	beta-N-acetylhexosaminidase-like domain	Hyaluronidase N-terminal domain-like	Hyaluronidase N-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
B	d2v5cb3	All alpha proteins	Hyaluronidase domain-like	Hyaluronidase post-catalytic domain-like	Hyaluronidase post-catalytic domain-like	Hyaluronidase, post-catalytic domain 3	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
B	d2v5cb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	alpha-D-glucuronidase/Hyaluronidase catalytic domain	Hyaluronidase catalytic domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
B	d2v5cb1	Alpha and beta proteins (a+b)	Zincin-like	beta-N-acetylhexosaminidase-like domain	Hyaluronidase N-terminal domain-like	Hyaluronidase N-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	(Trans)glycosidases	8038623	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Hyaluronidase post-catalytic domain-like	8038622	3001475	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-N-acetylhexosaminidase-like domain	8038626	3000192	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-N-acetylhexosaminidase-like domain	8038626	3000192	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8038623	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Hyaluronidase post-catalytic domain-like	8038622	3001475	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	PF21774	e2v5cA1	A: alpha bundles	X: Hyaluronidase domain-like	H: Hyaluronidase post-catalytic domain-like (From Topology)	T: Hyaluronidase post-catalytic domain-like	F: PF21774	ECOD (1.6)
A	PF07555	e2v5cA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF07555	ECOD (1.6)
A	PF02838	e2v5cA3	A: mixed a+b and a/b	X: Zincin-like	H: beta-N-acetylhexosaminidase-like domain (From Topology)	T: beta-N-acetylhexosaminidase-like domain	F: PF02838	ECOD (1.6)
B	PF21774	e2v5cB1	A: alpha bundles	X: Hyaluronidase domain-like	H: Hyaluronidase post-catalytic domain-like (From Topology)	T: Hyaluronidase post-catalytic domain-like	F: PF21774	ECOD (1.6)
B	PF07555	e2v5cB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF07555	ECOD (1.6)
B	PF02838	e2v5cB3	A: mixed a+b and a/b	X: Zincin-like	H: beta-N-acetylhexosaminidase-like domain (From Topology)	T: beta-N-acetylhexosaminidase-like domain	F: PF02838	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.379.10	Alpha Beta	2-Layer Sandwich	Chitobiase	domain 2	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	1.20.58.460	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	3.30.379.10	Alpha Beta	2-Layer Sandwich	Chitobiase	domain 2	CATH (4.3.0)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
B	1.20.58.460	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21774	Hyaluronidase post-catalytic domain-like (NagJ_C)	Hyaluronidase post-catalytic domain-like	This domain is located at the C-terminus of proteins that are members of family 84 glycoside hydrolases.These enzymes directly hydrolyse O-GlcNAcylated peptides/proteins. This domain folds into a five helical bundle with up-and-down topology. It may ...	This domain is located at the C-terminus of proteins that are members of family 84 glycoside hydrolases.These enzymes directly hydrolyse O-GlcNAcylated peptides/proteins. This domain folds into a five helical bundle with up-and-down topology. It may function in substrate binding or recognition.	Domain
A, B	PF02838	Glycosyl hydrolase family 20, domain 2 (Glyco_hydro_20b)	Glycosyl hydrolase family 20, domain 2	This domain has a zincin-like fold.	Domain
A, B	PF07555	beta-N-acetylglucosaminidase (NAGidase)	beta-N-acetylglucosaminidase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	O-GLCNACASE NAGJ	binding carbohydrate binding hydrolase activity, acting on glycosyl bonds hexosaminidase activity beta-N-acetylhexosaminidase activity beta-N-acetylglucosaminidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity	carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process organonitrogen compound metabolic process carbohydrate derivative metabolic process glycoprotein metabolic process macromolecule modification protein deglycosylation protein metabolic process macromolecule metabolic process protein modification process catabolic process carbohydrate catabolic process carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process organonitrogen compound metabolic process carbohydrate derivative metabolic process glycoprotein metabolic process macromolecule modification protein deglycosylation protein metabolic process macromolecule metabolic process protein modification process catabolic process carbohydrate catabolic process macromolecule catabolic process polysaccharide metabolic process polysaccharide catabolic process organic substance catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B	IPR003961	Fibronectin type III	Domain
A, B	IPR029018	Beta-hexosaminidase-like, domain 2	Homologous Superfamily
A, B	IPR011496	Beta-N-acetylglucosaminidase, catalytic domain	Domain
A, B	IPR008965	CBM2/CBM3, carbohydrate-binding domain superfamily	Homologous Superfamily
A, B	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B	IPR002102	Cellulosome anchoring protein, cohesin domain	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR000421	Coagulation factor 5/8 C-terminal domain	Domain
A, B	IPR015882	Beta-hexosaminidase, bacterial type, N-terminal	Domain
A, B	IPR049019	NagJ-like, helical domain	Domain
A, B	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.