3WFZ

Crystal structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase C236Y Mutant

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)
B	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8054008	3001405	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8054007	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8054009	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8054009	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Trans)glycosidases	8054007	3000313	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8054008	3001405	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8054008	3001405	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Trans)glycosidases	8054007	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8054009	3001528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8054008	3001405	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8054007	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8054009	3001528	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)
B	LBP_C	e3wfzB2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: LBP_C	ECOD (1.6)
B	Lact_bio_phlase	e3wfzB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Lact_bio_phlase	ECOD (1.6)
B	LBP_M	e3wfzB3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: LBP_M	ECOD (1.6)
C	LBP_C	e3wfzC2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: LBP_C	ECOD (1.6)
C	Lact_bio_phlase	e3wfzC3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Lact_bio_phlase	ECOD (1.6)
C	LBP_M	e3wfzC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: LBP_M	ECOD (1.6)
D	LBP_C	e3wfzD3	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: LBP_C	ECOD (1.6)
D	Lact_bio_phlase	e3wfzD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Lact_bio_phlase	ECOD (1.6)
D	LBP_M	e3wfzD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: LBP_M	ECOD (1.6)
A	LBP_C	e3wfzA2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: LBP_C	ECOD (1.6)
A	Lact_bio_phlase	e3wfzA3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Lact_bio_phlase	ECOD (1.6)
A	LBP_M	e3wfzA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: LBP_M	ECOD (1.6)

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	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
B	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
C	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
C	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
D	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
D	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	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, B, C, D	PF17385	Lacto-N-biose phosphorylase central domain (LBP_M)	Lacto-N-biose phosphorylase central domain	The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (EC:2.4.1.211), unlike either glycoside hydrolases or glyc ...	The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (EC:2.4.1.211), unlike either glycoside hydrolases or glycoside lyase. Intestinal colonisation by bifidobacteria is important for human health, especially in pediatrics, because colonisation seems to prevent infection by some pathogenic bacteria that cause diarrhoea or other illnesses. The operon seems to be involved in intestinal colonisation by bifidobacteria mediated by metabolism of mucin sugars. In addition, it may also resolve the question of the nature of the bifidus factor in human milk as the lacto-N-biose structure found in milk oligosaccharides.	Domain
A, B, C, D	PF17386	Lacto-N-biose phosphorylase C-terminal domain (LBP_C)	Lacto-N-biose phosphorylase C-terminal domain	The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (EC:2.4.1.211), unlike either glycoside hydrolases or glyc ...	The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (EC:2.4.1.211), unlike either glycoside hydrolases or glycoside lyase. Intestinal colonisation by bifidobacteria is important for human health, especially in pediatrics, because colonisation seems to prevent infection by some pathogenic bacteria that cause diarrhoea or other illnesses. The operon seems to be involved in intestinal colonisation by bifidobacteria mediated by metabolism of mucin sugars. In addition, it may also resolve the question of the nature of the bifidus factor in human milk as the lacto-N-biose structure found in milk oligosaccharides.	Domain
A, B, C, D	PF09508	Lacto-N-biose phosphorylase N-terminal TIM barrel domain (Lact_bio_phlase)	Lacto-N-biose phosphorylase N-terminal TIM barrel domain	The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (EC:2.4.1.211), unlike either glycoside hydrolases or glyc ...	The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (EC:2.4.1.211), unlike either glycoside hydrolases or glycoside lyase. Intestinal colonisation by bifidobacteria is important for human health, especially in pediatrics, because colonisation seems to prevent infection by some pathogenic bacteria that cause diarrhoea or other illnesses. The operon seems to be involved in intestinal colonisation by bifidobacteria mediated by metabolism of mucin sugars. In addition, it may also resolve the question of the nature of the bifidus factor in human milk as the lacto-N-biose structure found in milk oligosaccharides.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Lacto-N-biose phosphorylase	1,3-beta-galactosyl-N-acetylhexosamine phosphorylase activity glycosyltransferase activity transferase activity hexosyltransferase activity catalytic activity 1,4-alpha-oligoglucan phosphorylase activity	carbohydrate metabolic process primary metabolic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
A, B, C, D	IPR035080	Lacto-N-biose phosphorylase-like, N-terminal TIM barrel domain	Domain
A, B, C, D	IPR035356	Lacto-N-biose phosphorylase, C-terminal domain	Domain
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR035363	Lacto-N-biose phosphorylase, central domain	Domain
A, B, C, D	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily
A, B, C, D	IPR012711	Lacto-N-biose phosphorylase/D-galactosyl-beta-1->4-L-rhamnose phosphorylase	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.