Annotations: 4JKM

Crystal Structure of Clostridium perfringens beta-glucuronidase

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)
C [auth D]	d4jkmd1	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	D-maltodextrin-binding protein, MBP	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C [auth D]	d4jkmd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4jkmb2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	automated matches	automated matches	(Clostridium perfringens str. 13 ) [TaxId: 195102 ],	SCOPe (2.08)
B	d4jkmb1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	automated matches	(Clostridium perfringens str. 13 ) [TaxId: 195102 ],	SCOPe (2.08)
B	d4jkmb3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Clostridium perfringens str. 13 ) [TaxId: 195102 ],	SCOPe (2.08)
B	d4jkmb4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Clostridium perfringens str. 13 ) [TaxId: 195102 ],	SCOPe (2.08)
A	d4jkma2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	automated matches	automated matches	(Clostridium perfringens str. 13 ) [TaxId: 195102 ],	SCOPe (2.08)
A	d4jkma1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	automated matches	(Clostridium perfringens str. 13 ) [TaxId: 195102 ],	SCOPe (2.08)
A	d4jkma3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	automated matches	automated matches	(Clostridium perfringens str. 13 ) [TaxId: 195102 ],	SCOPe (2.08)
A	d4jkma4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Clostridium perfringens str. 13 ) [TaxId: 195102 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth D]	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	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)
D [auth C]	EryCIII-like_N	e4jkmC1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: EryCIII-like_N	ECOD (v294.1)
C [auth D]	SBP_bac_1	e4jkmD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v294.1)
B	V-set	e4jkmB1	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: V-set	ECOD (v294.1)
A	V-set	e4jkmA1	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth D]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth D], D [auth C]	PF01547	Bacterial extracellular solute-binding protein (SBP_bac_1)	Bacterial extracellular solute-binding protein	-	Family
A, B	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	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	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
C [auth D], D [auth C]	Maltose-binding periplasmic protein	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex extracellular region ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex extracellular region periplasmic space outer membrane-bounded periplasmic space cell envelope
A, B	Beta-glucuronidase	binding carbohydrate binding hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds beta-glucuronidase activity glucuronidase activity hydrolase activity catalytic activity	carbohydrate metabolic process primary metabolic process metabolic process cellular process glycoside catabolic process carbohydrate derivative catabolic process catabolic process glycoside metabolic process carbohydrate derivative metabolic process glycosyl compound catabolic process glucuronoside catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D], D [auth C]	IPR006061	Solute-binding family 1, conserved site	Conserved Site
C [auth D], D [auth C]	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
C [auth D], D [auth C]	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A, B	IPR006102	Glycoside hydrolase family 2, immunoglobulin-like beta-sandwich	Domain
A, B	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B	IPR006101	Glycoside hydrolase, family 2	Family
A, B	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B	IPR036156	Beta-Galactosidase/glucuronidase domain superfamily	Homologous Superfamily
A, B	IPR006104	Glycosyl hydrolases family 2, sugar binding domain	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR006103	Glycoside hydrolase family 2, catalytic domain	Domain
A, B	IPR023232	Glycoside hydrolase, family 2, active site	Active Site
A, B	IPR023230	Glycoside hydrolase, family 2, conserved site	Conserved Site

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.