1YIF

CRYSTAL STRUCTURE OF beta-1,4-xylosidase FROM BACILLUS SUBTILIS, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

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	d1yifa1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Beta-D-xylosidase C-terminal domain-like	Beta-D-xylosidase C-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1yifa2	All beta proteins	5-bladed beta-propeller	Arabinanase/levansucrase/invertase	alpha-L-arabinanase-like	Beta-D-xylosidase N-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1yifb1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Beta-D-xylosidase C-terminal domain-like	Beta-D-xylosidase C-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1yifb2	All beta proteins	5-bladed beta-propeller	Arabinanase/levansucrase/invertase	alpha-L-arabinanase-like	Beta-D-xylosidase N-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1yifc1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Beta-D-xylosidase C-terminal domain-like	Beta-D-xylosidase C-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1yifc2	All beta proteins	5-bladed beta-propeller	Arabinanase/levansucrase/invertase	alpha-L-arabinanase-like	Beta-D-xylosidase N-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1yifd1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Beta-D-xylosidase C-terminal domain-like	Beta-D-xylosidase C-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1yifd2	All beta proteins	5-bladed beta-propeller	Arabinanase/levansucrase/invertase	alpha-L-arabinanase-like	Beta-D-xylosidase N-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	beta-D-xylosidase C-terminal domain-like	8022156	4001673	SCOP2 (2022-06-29)
A	SCOP2 Family	alpha-L-arabinanase-like	8022158	4002120	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Concanavalin A-like lectins/glucanases	8034536	3000120	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Furanosidase-like	8034538	3000845	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8034536	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Furanosidase-like	8034538	3000845	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8034536	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Furanosidase-like	8034538	3000845	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8034536	3000120	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Furanosidase-like	8034538	3000845	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	DUF1349_1	e1yifA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: DUF1349_1	ECOD (1.6)
A	Glyco_hydro_43	e1yifA2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 5-bladed	F: Glyco_hydro_43	ECOD (1.6)
B	DUF1349_1	e1yifB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: DUF1349_1	ECOD (1.6)
B	Glyco_hydro_43	e1yifB2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 5-bladed	F: Glyco_hydro_43	ECOD (1.6)
C	DUF1349_1	e1yifC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: DUF1349_1	ECOD (1.6)
C	Glyco_hydro_43	e1yifC2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 5-bladed	F: Glyco_hydro_43	ECOD (1.6)
D	DUF1349_1	e1yifD1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: DUF1349_1	ECOD (1.6)
D	Glyco_hydro_43	e1yifD2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 5-bladed	F: Glyco_hydro_43	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
A	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
B	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
C	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
D	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF04616	Glycosyl hydrolases family 43 (Glyco_hydro_43)	Glycosyl hydrolases family 43	-	Repeat
A, B, C, D	PF17851	Beta xylosidase C-terminal Concanavalin A-like domain (GH43_C2)	Beta xylosidase C-terminal Concanavalin A-like domain	This domain is found to the C-terminus of the Pfam:PF04616 domain. This domain adopts a concanavalin A-like fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	BETA-1,4-XYLOSIDASE	xylanase activity hydrolase activity, acting on glycosyl bonds xylan 1,4-beta-xylosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity	carbohydrate metabolic process xylan catabolic process catabolic process hemicellulose metabolic process cell wall organization or biogenesis carbohydrate catabolic process hemicellulose catabolic process primary metabolic process macromolecule catabolic process cell wall macromolecule catabolic process xylan metabolic process polysaccharide metabolic process polysaccharide catabolic process metabolic process carbohydrate metabolic process xylan catabolic process catabolic process hemicellulose metabolic process cell wall organization or biogenesis carbohydrate catabolic process hemicellulose catabolic process primary metabolic process macromolecule catabolic process cell wall macromolecule catabolic process xylan metabolic process polysaccharide metabolic process polysaccharide catabolic process metabolic process cellular process macromolecule metabolic process cell wall polysaccharide metabolic process cell wall macromolecule metabolic process cell wall polysaccharide catabolic process	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B, C, D	IPR023296	Glycosyl hydrolase, five-bladed beta-propeller domain superfamily	Homologous Superfamily
A, B, C, D	IPR006710	Glycoside hydrolase, family 43	Family
A, B, C, D	IPR041542	Beta-xylosidase, C-terminal Concanavalin A-like domain	Domain
A, B, C, D	IPR051795	Glycosyl Hydrolase Family 43	Family

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.