3E80 | pdb_00003e80

Structure of Heparinase II complexed with heparan sulfate degradation disaccharide product

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8090364	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Galactose mutarotase-like	8090362	3000035	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Chondroitin AC/alginate lyase	8090361	3001005	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Galactose mutarotase-like	8090362	3000035	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8090364	3001528	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Chondroitin AC/alginate lyase	8090361	3001005	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8090364	3001528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Galactose mutarotase-like	8090362	3000035	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Chondroitin AC/alginate lyase	8090361	3001005	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)
C	EUF07810	e3e80C1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: EUF07810	ECOD (1.6)
C	Hepar_II_III	e3e80C2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Hepar_II_III	ECOD (1.6)
C	Alginate_lyase_1	e3e80C3	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Alginate_lyase_1	ECOD (1.6)
B	EUF07810	e3e80B1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: EUF07810	ECOD (1.6)
B	Hepar_II_III	e3e80B2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Hepar_II_III	ECOD (1.6)
B	Alginate_lyase_1	e3e80B3	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Alginate_lyase_1	ECOD (1.6)
A	EUF07810	e3e80A1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: EUF07810	ECOD (1.6)
A	Hepar_II_III	e3e80A2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Hepar_II_III	ECOD (1.6)
A	Alginate_lyase_1	e3e80A3	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Alginate_lyase_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.50.10.100	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase	Chondroitin AC/alginate lyase	CATH (4.3.0)
C	2.70.98.70	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
C	2.60.40.2750	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B	1.50.10.100	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase	Chondroitin AC/alginate lyase	CATH (4.3.0)
B	2.70.98.70	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
B	2.60.40.2750	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	1.50.10.100	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase	Chondroitin AC/alginate lyase	CATH (4.3.0)
A	2.70.98.70	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
A	2.60.40.2750	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF18675	Heparinase II C-terminal domain (HepII_C)	Heparinase II C-terminal domain	Heparinase II (HepII) is an 85-kDa dimeric enzyme that depolymerizes both heparin and heparan sulfate glycosaminoglycans [1]. The protein is composed of three domains: an N-terminal alpha-helical domain, a central two-layered beta-sheet domain, and a ...	Heparinase II (HepII) is an 85-kDa dimeric enzyme that depolymerizes both heparin and heparan sulfate glycosaminoglycans [1]. The protein is composed of three domains: an N-terminal alpha-helical domain, a central two-layered beta-sheet domain, and a C-terminal domain forming a two-layered beta-sheet. The C-terminal domain contains nine beta-strands packed together in a manner resembling a beta-barrel [2].	Domain
A, B, C	PF16332	Domain of unknown function (DUF4962) (DUF4962)	Domain of unknown function (DUF4962)	-	Repeat
A, B, C	PF07940	Heparinase II/III-like, C-terminal (Hepar_II_III_C)	Heparinase II/III-like, C-terminal	This is the C-terminal domain of Heparin and heparin-sulfate lyase (HepB, also known as heparinase II), Heparin-sulfate lyase (HepC, also known as heparinase III and distantly related sequences. The structures of Heparinase II and III have been solve ...	This is the C-terminal domain of Heparin and heparin-sulfate lyase (HepB, also known as heparinase II), Heparin-sulfate lyase (HepC, also known as heparinase III and distantly related sequences. The structures of Heparinase II and III have been solved [3,4]. HepB cleaves both heparin and heparan sulfate glycosaminoglycans. HepC specifically cleaves heparan sulfate-rich regions of acidic polysaccharides, it does not act on N,O-desulfated glucosamine or N-acetyl-O-sulfated glucosamine linkages. HepC functions in cleaving metazoan heparan sulfate and providing carbon, nitrogen and sulfate sources for microorganisms [1-4]. This entry also includes FtsZ-localized protein C (FzlC), which binds and recruits FtsZ polymers to membranes early in the cell cycle. It may also improve the efficiency of cytokinesis. This protein has been reported to have sequence similarity to heparinase II/III family proteins [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Heparinase II protein	heparin-sulfate lyase activity lyase activity carbon-oxygen lyase activity, acting on polysaccharides catalytic activity carbon-oxygen lyase activity cation binding ion binding binding metal ion binding small molecule binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding heparin-sulfate lyase activity lyase activity carbon-oxygen lyase activity, acting on polysaccharides catalytic activity carbon-oxygen lyase activity cation binding ion binding binding metal ion binding small molecule binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding heparin lyase activity	carbohydrate derivative catabolic process glycoprotein catabolic process catabolic process heparin proteoglycan catabolic process carbohydrate derivative metabolic process primary metabolic process protein catabolic process glycoprotein metabolic process macromolecule catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process proteoglycan catabolic process carbohydrate derivative catabolic process glycoprotein catabolic process catabolic process heparin proteoglycan catabolic process carbohydrate derivative metabolic process primary metabolic process protein catabolic process glycoprotein metabolic process macromolecule catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process proteoglycan catabolic process proteoglycan metabolic process heparin proteoglycan metabolic process	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR032518	Heparinase II, N-terminal	Domain
A, B, C	IPR054645	Heparin/heparin-sulfate lyase HepB	Family
A, B, C	IPR008929	Chondroitin AC/alginate lyase	Homologous Superfamily
A, B, C	IPR040925	Heparinase II, C-terminal	Domain
A, B, C	IPR012480	Heparinase II/III-like, C-terminal	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.