2YA1 | pdb_00002ya1

Product complex of a multi-modular glycogen-degrading pneumococcal virulence factor SpuA

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	SCOP2B Superfamily	Starch-binding domain-like	8034620	3000816	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Starch-binding domain-like	8034619	3000816	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	XPG_N,XPG_I	e2ya1A1	A: alpha bundles	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: XPG_N,XPG_I	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.1110	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	2.60.40.1220	Mainly Beta	Sandwich	Immunoglobulin-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)
A	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02922	Carbohydrate-binding module 48 (Isoamylase N-terminal domain) (CBM_48)	Carbohydrate-binding module 48 (Isoamylase N-terminal domain)	This domain is found in a range of enzymes that act on branched substrates - isoamylase, pullulanase and branching enzyme. This family also contains the beta subunit of 5' AMP activated kinase.	Domain
A	PF18033	SpuA C-terminal (SpuA_C)	SpuA C-terminal	This is the C-terminal beta sandwich domain found in Streptococcus pneumoniae Spu4 proteins. Spu4 is a large multimodular cell wall-attached enzyme involved in the degradation of glycogen [1].	Domain
A	PF00128	Alpha amylase, catalytic domain (Alpha-amylase)	Alpha amylase, catalytic domain	Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, a ...	Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain.	Domain
A	PF03714	Bacterial pullanase-associated domain (PUD)	Bacterial pullanase-associated domain	Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C terminii of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrat ...	Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C terminii of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrate binding function.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PUTATIVE ALKALINE AMYLOPULLULANASE	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity limit dextrinase activity catalytic activity polysaccharide binding carbohydrate binding glycogen binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity limit dextrinase activity catalytic activity polysaccharide binding carbohydrate binding glycogen binding pullulanase activity pullulan binding amylopectin binding carbohydrate derivative binding	carbohydrate metabolic process glucan biosynthetic process polysaccharide biosynthetic process carbohydrate biosynthetic process primary metabolic process macromolecule biosynthetic process alpha-glucan metabolic process polysaccharide metabolic process glucan metabolic process biosynthetic process alpha-glucan biosynthetic process metabolic process cellular process macromolecule metabolic process	cell surface cellular anatomical structure

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013784	Carbohydrate-binding-like fold	Homologous Superfamily
A	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A	IPR019931	LPXTG cell wall anchor motif	Conserved Site
A	IPR005323	Pullulanase, carbohydrate-binding module 41	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR005877	YSIRK Gram-positive signal peptide	Domain
A	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A	IPR011838	Pullulanase, extracellular	Domain
A	IPR006047	Glycosyl hydrolase family 13, catalytic domain	Domain
A	IPR014755	Copper resistance protein CopC/internalin, immunoglobulin-like	Homologous Superfamily
A	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily
A	IPR004193	Glycoside hydrolase, family 13, N-terminal	Domain
A	IPR040806	SpuA, C-terminal	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.