6S0S

The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, ribostamycin B and 2-oxoglutarate

External Resource: Annotation

Domain Annotation: ECOD Classification
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	PhyH_1	e6s0sB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)
D	PhyH_1	e6s0sD1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)
E	PhyH_1	e6s0sE1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)
A	PhyH_1	e6s0sA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)
C	PhyH_1	e6s0sC1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)
F	PhyH_1	e6s0sF1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF05721	Phytanoyl-CoA dioxygenase (PhyH) (PhyH)	Phytanoyl-CoA dioxygenase (PhyH)	This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficie ...	This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Kanamycin B dioxygenase	oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity	aminoglycoside antibiotic biosynthetic process glycosyl compound metabolic process organic hydroxy compound metabolic process carbohydrate derivative metabolic process alcohol metabolic process antibiotic biosynthetic process antibiotic metabolic process polyol biosynthetic process small molecule metabolic process carbohydrate derivative biosynthetic process kanamycin metabolic process polyol metabolic process glycosyl compound biosynthetic process small molecule biosynthetic process aminoglycoside antibiotic biosynthetic process glycosyl compound metabolic process organic hydroxy compound metabolic process carbohydrate derivative metabolic process alcohol metabolic process antibiotic biosynthetic process antibiotic metabolic process polyol biosynthetic process small molecule metabolic process carbohydrate derivative biosynthetic process kanamycin metabolic process polyol metabolic process glycosyl compound biosynthetic process small molecule biosynthetic process glycoside metabolic process kanamycin biosynthetic process glycoside biosynthetic process aminoglycoside antibiotic metabolic process biosynthetic process organic hydroxy compound biosynthetic process alcohol biosynthetic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR051961	Fungal Secondary Metabolite Dioxygenase	Family
A, B, C, D, E A, B, C, D, E, F	IPR008775	Phytanoyl-CoA dioxygenase-like	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.