3AC0 | pdb_00003ac0

Crystal structure of Beta-glucosidase from Kluyveromyces marxianus in complex with glucose

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)
D	d3ac0d4	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin III-like	Fibronectin III-like	Beta-glucosidase C-terminal domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
D	d3ac0d3	All beta proteins	Anthrax protective antigen N-terminal-like	PA14-like	PA14	Beta-glucosidase PA14 domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
D	d3ac0d1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	NagZ-like	Beta-glucosidase	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
D	d3ac0d2	Alpha and beta proteins (a/b)	Flavodoxin-like	Beta-D-glucan exohydrolase, C-terminal domain-like	Beta-D-glucan exohydrolase, C-terminal domain-like	Beta-glucosidase middle domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
C	d3ac0c4	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin III-like	Fibronectin III-like	Beta-glucosidase C-terminal domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
C	d3ac0c3	All beta proteins	Anthrax protective antigen N-terminal-like	PA14-like	PA14	Beta-glucosidase PA14 domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
C	d3ac0c1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	NagZ-like	Beta-glucosidase	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
C	d3ac0c2	Alpha and beta proteins (a/b)	Flavodoxin-like	Beta-D-glucan exohydrolase, C-terminal domain-like	Beta-D-glucan exohydrolase, C-terminal domain-like	Beta-glucosidase middle domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
B	d3ac0b4	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin III-like	Fibronectin III-like	Beta-glucosidase C-terminal domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
B	d3ac0b3	All beta proteins	Anthrax protective antigen N-terminal-like	PA14-like	PA14	Beta-glucosidase PA14 domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
B	d3ac0b1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	NagZ-like	Beta-glucosidase	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
B	d3ac0b2	Alpha and beta proteins (a/b)	Flavodoxin-like	Beta-D-glucan exohydrolase, C-terminal domain-like	Beta-D-glucan exohydrolase, C-terminal domain-like	Beta-glucosidase middle domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
A	d3ac0a4	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin III-like	Fibronectin III-like	Beta-glucosidase C-terminal domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
A	d3ac0a3	All beta proteins	Anthrax protective antigen N-terminal-like	PA14-like	PA14	Beta-glucosidase PA14 domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
A	d3ac0a1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	NagZ-like	Beta-glucosidase	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)
A	d3ac0a2	Alpha and beta proteins (a/b)	Flavodoxin-like	Beta-D-glucan exohydrolase, C-terminal domain-like	Beta-D-glucan exohydrolase, C-terminal domain-like	Beta-glucosidase middle domain	Yeast (Kluyveromyces marxianus ) [TaxId: 4911 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Fn3-like	e3ac0D2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Fn3-like	ECOD (1.6)
D	PA14	e3ac0D1	A: beta sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen (From Topology)	H: N-terminal beta-sandwich domain in anthrax protective antigen (From Topology)	T: N-terminal beta-sandwich domain in anthrax protective antigen	F: PA14	ECOD (1.6)
D	Glyco_hydro_3	e3ac0D4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_3	ECOD (1.6)
D	Glyco_hydro_3_C	e3ac0D5	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Beta-D-glucan exohydrolase, C-terminal domain (From Topology)	T: Beta-D-glucan exohydrolase, C-terminal domain	F: Glyco_hydro_3_C	ECOD (1.6)
C	Fn3-like	e3ac0C2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Fn3-like	ECOD (1.6)
C	PA14	e3ac0C4	A: beta sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen (From Topology)	H: N-terminal beta-sandwich domain in anthrax protective antigen (From Topology)	T: N-terminal beta-sandwich domain in anthrax protective antigen	F: PA14	ECOD (1.6)
C	Glyco_hydro_3	e3ac0C1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_3	ECOD (1.6)
C	Glyco_hydro_3_C	e3ac0C3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Beta-D-glucan exohydrolase, C-terminal domain (From Topology)	T: Beta-D-glucan exohydrolase, C-terminal domain	F: Glyco_hydro_3_C	ECOD (1.6)
B	Fn3-like	e3ac0B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Fn3-like	ECOD (1.6)
B	PA14	e3ac0B3	A: beta sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen (From Topology)	H: N-terminal beta-sandwich domain in anthrax protective antigen (From Topology)	T: N-terminal beta-sandwich domain in anthrax protective antigen	F: PA14	ECOD (1.6)
B	Glyco_hydro_3	e3ac0B4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_3	ECOD (1.6)
B	Glyco_hydro_3_C	e3ac0B1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Beta-D-glucan exohydrolase, C-terminal domain (From Topology)	T: Beta-D-glucan exohydrolase, C-terminal domain	F: Glyco_hydro_3_C	ECOD (1.6)
A	Fn3-like	e3ac0A4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Fn3-like	ECOD (1.6)
A	PA14	e3ac0A3	A: beta sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen (From Topology)	H: N-terminal beta-sandwich domain in anthrax protective antigen (From Topology)	T: N-terminal beta-sandwich domain in anthrax protective antigen	F: PA14	ECOD (1.6)
A	Glyco_hydro_3	e3ac0A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_3	ECOD (1.6)
A	Glyco_hydro_3_C	e3ac0A2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Beta-D-glucan exohydrolase, C-terminal domain (From Topology)	T: Beta-D-glucan exohydrolase, C-terminal domain	F: Glyco_hydro_3_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.20.20.300	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycoside hydrolase, family 3, N-terminal domain	CATH (4.3.0)
D	3.40.50.1700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Glycoside hydrolase family 3 C-terminal domain	CATH (4.3.0)
D	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	3.20.20.300	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycoside hydrolase, family 3, N-terminal domain	CATH (4.3.0)
C	3.40.50.1700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Glycoside hydrolase family 3 C-terminal domain	CATH (4.3.0)
C	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.20.20.300	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycoside hydrolase, family 3, N-terminal domain	CATH (4.3.0)
B	3.40.50.1700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Glycoside hydrolase family 3 C-terminal domain	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)
A	3.20.20.300	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycoside hydrolase, family 3, N-terminal domain	CATH (4.3.0)
A	3.40.50.1700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Glycoside hydrolase family 3 C-terminal domain	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF07691	PA14 domain (PA14)	PA14 domain	This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dic ...	This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium prespore-cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding.	Domain
A, B, C, D	PF00933	Glycosyl hydrolase family 3 N terminal domain (Glyco_hydro_3)	Glycosyl hydrolase family 3 N terminal domain		Domain
A, B, C, D	PF01915	Glycosyl hydrolase family 3 C-terminal domain (Glyco_hydro_3_C)	Glycosyl hydrolase family 3 C-terminal domain	This domain is involved in catalysis and may be involved in binding beta-glucan [1]. This domain is found associated with Pfam:PF00933.	Domain
A, B, C, D	PF14310	Fibronectin type III-like domain (Fn3-like)	Fibronectin type III-like domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Beta-glucosidase I	hydrolase activity, acting on glycosyl bonds glucosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity beta-glucosidase activity catalytic activity	carbohydrate metabolic process catabolic process glucan catabolic process beta-glucan metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process beta-glucan catabolic process polysaccharide catabolic process metabolic process cellular process cellulose catabolic process carbohydrate metabolic process catabolic process glucan catabolic process beta-glucan metabolic process carbohydrate catabolic process primary metabolic process macromolecule catabolic process polysaccharide metabolic process glucan metabolic process beta-glucan catabolic process polysaccharide catabolic process metabolic process cellular process cellulose catabolic process macromolecule metabolic process cellulose metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050288	Cellulose-degrading glycosyl hydrolase 3	Family
A, B, C, D	IPR001764	Glycoside hydrolase, family 3, N-terminal	Domain
A, B, C, D	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C, D	IPR002772	Glycoside hydrolase family 3 C-terminal domain	Domain
A, B, C, D	IPR036962	Glycoside hydrolase, family 3, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR011658	PA14 domain	Domain
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR019800	Glycoside hydrolase, family 3, active site	Active Site
A, B, C, D	IPR037524	PA14/GLEYA domain	Domain
A, B, C, D	IPR026891	Fibronectin type III-like domain	Domain
A, B, C, D	IPR036881	Glycoside hydrolase family 3 C-terminal domain superfamily	Homologous Superfamily

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.