4BQ4 | pdb_00004bq4

Structural analysis of an exo-beta-agarase

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e4bq4B1	A: P-loop domains-like	X: Metalloproteases (zincins) catalytic domain	H: Metalloproteases (zincins) catalytic domain	T: Peptidase_M2	F:	ECOD (20:10:01)
A		e4bq4A1	A: immunoglobulin/albumin-binding domain-like	X: EGF-related	H: Complement control module/SCR domain	T: Glyco_hydro_42	F:	ECOD (20:10:01)
A		e4bq4A2	A: immunoglobulin/albumin-binding domain-like	X: EGF-related	H: Complement control module/SCR domain	T: tRNA_anti-codon	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.430	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding lectin	CATH (4.3.0)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	2.60.120.430	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding lectin	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02449	Beta-galactosidase (Glyco_hydro_42)	Beta-galactosidase	This group of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. The enzyme catalyses the hydrolysis of terminal, non-reducing terminal beta-D-galactosidase residues.	Domain
A, B	PF17992	Agarase CBM like domain (Agarase_CBM)	Agarase CBM like domain	This is the N-terminal CBM-like domain in exo-beta-agarase proteins (EC:3.2.1.81) found in the marine microbe Saccharophagus degradans. This enzyme catalyzes a critical step in the metabolism of agarose by S. degradans through cleaving agarose oligom ...	This is the N-terminal CBM-like domain in exo-beta-agarase proteins (EC:3.2.1.81) found in the marine microbe Saccharophagus degradans. This enzyme catalyzes a critical step in the metabolism of agarose by S. degradans through cleaving agarose oligomers into neoagarobiose products that can be further processed into monomers. The CBM-like domain is structurally very similar to some CBM families. A loop in the CBM-like domain is involved in forming the roof of the active site channel. The contribution of the CBM-like domain to formation of the active site of the enzyme supports a role in substrate recognition explaining the exo-mode of beta-agarase action [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	B-AGARASE	hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity beta-agarase activity catalytic activity beta-galactosidase activity galactosidase activity cation binding ion binding binding metal ion binding small molecule binding	carbohydrate metabolic process primary metabolic process metabolic process cellular process	protein-containing complex catalytic complex beta-galactosidase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR040669	Agarase, CBM-like domain	Domain
A, B	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B	IPR013529	Glycoside hydrolase, family 42, N-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.