2VTF | pdb_00002vtf

X-ray crystal structure of the Endo-beta-N-acetylglucosaminidase from Arthrobacter protophormiae E173Q mutant reveals a TIM barrel catalytic domain and two ancillary domains

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	SCOP2B Superfamily	Fibronectin type III	8051925	3002063	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	galactose-binding domain-like	8051923	3000087	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8051921	3000313	SCOP2B (2022-06-29)
A	SCOP2 Family	GH85 catalytic domain-like	8044661	4004066	SCOP2 (2022-06-29)
A	SCOP2 Family	GH85 putative CBM-like	8051922	4007574	SCOP2 (2022-06-29)
A	SCOP2 Family	Fibronectin type III	8051924	4007555	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	(Trans)glycosidases	8051921	3000313	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	galactose-binding domain-like	8051923	3000087	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Fibronectin type III	8051925	3002063	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e2vtfB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T:	F:	ECOD (20:10:01)
B		e2vtfB2	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: GH85_C	F:	ECOD (20:10:01)
B		e2vtfB3	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Methyltransf_25	F:	ECOD (20:10:01)
A		e2vtfA7	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: Melibiase_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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)
A	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	ENDO-BETA-N-ACETYLGLUCOSAMINIDASE	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity hydrolase activity, acting on glycosyl bonds 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 cellular process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR032979	Cytosolic endo-beta-N-acetylglucosaminidase	Family
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR005201	Cytosolic endo-beta-N-acetylglucosaminidase, TIM barrel domain	Domain
A, B	IPR054110	Endo-beta-N-acetylglucosaminidase D-like, D2 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.