2OKX

Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	alpha-L-rhamnosidase precatalytic domain-like	8047398	4005623	SCOP2 (2021-05-27)
A	SCOP2 Family	Alpha-L-rhamnosidase C-terminal domain-like	8046916	4005366	SCOP2 (2021-05-27)
A	SCOP2 Family	Alpha-L-rhamnosidase N-terminal domain-like	8050959	4007126	SCOP2 (2021-05-27)
A	SCOP2 Family	Alpha-L-rhamnosidase N-terminal domain-like	8051903	4007126	SCOP2 (2021-05-27)
A	SCOP2 Family	Bacterial alpha-L-rhamnosidase-like	8046913	4005365	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	galactose-binding domain-like	8051901	3000087	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	YicI C-terminal domain-like	8051900	3000267	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	Alpha-L-rhamnosidase associated domain -like	8051902	3002069	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	Alpha-L-rhamnosidase associated domain -like	8051904	3002069	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	Six-hairpin glycosidases	8051899	3000970	SCOP2 (2021-05-27)
B	SCOP2B Superfamily	galactose-binding domain-like	8051901	3000087	SCOP2B (2021-05-27)
B	SCOP2B Superfamily	Alpha-L-rhamnosidase associated domain -like	8051902	3002069	SCOP2B (2021-05-27)
B	SCOP2B Superfamily	Alpha-L-rhamnosidase associated domain -like	8051904	3002069	SCOP2B (2021-05-27)
B	SCOP2B Superfamily	YicI C-terminal domain-like	8051900	3000267	SCOP2B (2021-05-27)
B	SCOP2B Superfamily	Six-hairpin glycosidases	8051899	3000970	SCOP2B (2021-05-27)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF05592	e2okxA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PF05592	ECOD (1.6)
A	PF08531	e2okxA4	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PF08531	ECOD (1.6)
A	PF21557	e2okxA6	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF21557	ECOD (1.6)
A	PF17390	e2okxA3	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related (From Topology)	T: Glycoside hydrolase family 127 middle domain-related	F: PF17390	ECOD (1.6)
A	PF17389	e2okxA5	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: PF17389	ECOD (1.6)
B	PF05592	e2okxB2	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF05592	ECOD (1.6)
B	PF08531	e2okxB1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF08531	ECOD (1.6)
B	PF21557	e2okxB3	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF21557	ECOD (1.6)
B	PF17390	e2okxB5	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related (From Topology)	T: Glycoside hydrolase family 127 middle domain-related	F: PF17390	ECOD (1.6)
B	PF17389	e2okxB4	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: PF17389	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 (4.2.0)
A	2.60.420.10	Mainly Beta	Sandwich	Maltose phosphorylase, domain 3	Maltose phosphorylase, domain 3	CATH (4.2.0)
A	1.50.10.10	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.2.0)
B	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.2.0)
B	2.60.420.10	Mainly Beta	Sandwich	Maltose phosphorylase, domain 3	Maltose phosphorylase, domain 3	CATH (4.2.0)
B	1.50.10.10	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05592	Bacterial alpha-L-rhamnosidase concanavalin-like domain (Bac_rhamnosid)	Bacterial alpha-L-rhamnosidase concanavalin-like domain	This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are impo ...	This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria [1].	Domain
A, B	PF08531	Alpha-L-rhamnosidase N-terminal domain (Bac_rhamnosid_N)	Alpha-L-rhamnosidase N-terminal domain	This family consists of bacterial rhamnosidase A and B enzymes. This domain is probably involved in substrate recognition.	Domain
A, B	PF17389	Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain (Bac_rhamnosid6H)	Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain	-	Repeat
A, B	PF17390	Bacterial alpha-L-rhamnosidase C-terminal domain (Bac_rhamnosid_C)	Bacterial alpha-L-rhamnosidase C-terminal domain	This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are impo ...	This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria [1].	Domain
A, B	PF21557	Alpha-L-rhamnosidase, domain D2 (RhaB_D2)	Alpha-L-rhamnosidase, domain D2	This domain is found in Alpha-L-rhamnosidase from Bacillus sp. (RhaB), a member of glycoside hydrolase (GH) family 78 that catalyses the hydrolytic release of rhamnose from polysaccharides and glycosides, degrading the bacterial biofilm gellan. RhaB ...	This domain is found in Alpha-L-rhamnosidase from Bacillus sp. (RhaB), a member of glycoside hydrolase (GH) family 78 that catalyses the hydrolytic release of rhamnose from polysaccharides and glycosides, degrading the bacterial biofilm gellan. RhaB is organised into five domains: Pfam:PF08531, this entry, Pfam:PF05592, Pfam:PF17389 and Pfam:PF17390. This domain shows a beta-sandwich structure with 13 beta-strands and two short helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Rhamnosidase B	hydrolase activity, acting on glycosyl bonds alpha-L-rhamnosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	carbohydrate metabolic process primary metabolic process metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012341	Six-hairpin glycosidase-like superfamily	Homologous Superfamily
A, B	IPR035398	Alpha-L-rhamnosidase C-terminal domain	Domain
A, B	IPR035396	Alpha-L-rhamnosidase, six-hairpin glycosidase domain	Domain
A, B	IPR008928	Six-hairpin glycosidase superfamily	Homologous Superfamily
A, B	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B	IPR013737	Bacterial alpha-L-rhamnosidase N-terminal	Domain
A, B	IPR048653	Alpha-L-rhamnosidase, domain D2	Domain
A, B	IPR008902	Alpha-L-rhamnosidase, concanavalin-like domain	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 R01GM133198.