2VMF

Structural and biochemical evidence for a boat-like transition state in beta-mannosidases

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	d2vmfa1	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
A	d2vmfa4	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
A	d2vmfa5	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
B	d2vmfb1	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
B	d2vmfb4	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
B	d2vmfb5	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
B	d2vmfb6	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	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	8034628	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055217	3002047	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055472	3002047	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	galactose-binding domain-like	8034627	3000087	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055470	3002047	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055472	3002047	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055470	3002047	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	galactose-binding domain-like	8034627	3000087	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8034628	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055217	3002047	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	Glyco_hydro_2_N	e2vmfA1	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	e2vmfA2	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	EUF07702	e2vmfA4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: EUF07702	ECOD (1.6)
A	EUF07703	e2vmfA3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: EUF07703	ECOD (1.6)
A	Glyco_hydro_2_C	e2vmfA5	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	e2vmfB1	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	e2vmfB2	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	EUF07702	e2vmfB4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: EUF07702	ECOD (1.6)
B	EUF07703	e2vmfB3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: EUF07703	ECOD (1.6)
B	Glyco_hydro_2_C	e2vmfB5	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 (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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	PF17753	Ig-fold domain (Ig_mannosidase)	Ig-fold domain	This Ig-like fold domain is found in mannosidase enzymes [1].	Domain
A, B	PF17786	Mannosidase Ig/CBM-like domain (Mannosidase_ig)	Mannosidase Ig/CBM-like domain	This domain corresponds to domain 4 in the structure of Bacteroides thetaiotaomicron beta-mannosidase, BtMan2A [1]. This domain has an Ig-like fold.	Domain
A, B	PF22666	Glycosyl hydrolase 2 galactose-binding domain-like (Glyco_hydro_2_N2)	Glycosyl hydrolase 2 galactose-binding domain-like	This domain is found in a number of proteins belonging to glycosyl hydrolase 2 family [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	BETA-MANNOSIDASE	hydrolase activity, acting on glycosyl bonds beta-mannosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds mannosidase activity hydrolase activity catalytic activity	carbohydrate metabolic process primary metabolic process metabolic process cellular process carbohydrate derivative catabolic process glycoprotein catabolic process catabolic process carbohydrate derivative metabolic process protein catabolic process glycoprotein metabolic process macromolecule catabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B	IPR006102	Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich	Domain
A, B	IPR036156	Beta-Galactosidase/glucuronidase domain superfamily	Homologous Superfamily
A, B	IPR050887	Beta-mannosidase glycosyl hydrolases	Family
A, B	IPR041447	Mannosidase Ig/CBM-like domain	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR041625	Beta-mannosidase, Ig-fold domain	Domain
A, B	IPR054593	Beta-mannosidase-like, galactose-binding domain-like	Domain

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.