5JMD | pdb_00005jmd

Heparinase III-BT4657 gene product, Methylated Lysines

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)
A	SCOP2 Family	HepC N-terminal domain-like	8046308	4005012	SCOP2 (2022-06-29)
A	SCOP2 Family	Heparinase II/III-like	8050262	4006819	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Chondroitin AC/alginate lyase	8090369	3001005	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Galactose mutarotase-like	8090370	3000035	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)
A	Hepar_II_III	e5jmdA1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: Hepar_II_III	ECOD (1.6)
A	Hepar_II_III_N	e5jmdA2	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Hepar_II_III_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
A	PF16889	Heparinase II/III N-terminus (Hepar_II_III_N)	Heparinase II/III N-terminus	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Heparinase III protein	lyase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	-	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR054646	Heparin-sulfate lyase HepC	Family
A	IPR031680	Heparin-sulfate lyase, N-terminal	Domain
A	IPR008929	Chondroitin AC/alginate lyase	Homologous Superfamily
A	IPR012480	Heparinase II/III-like, C-terminal	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

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.