2HMK | pdb_00002hmk

Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene

External Resource: Annotation

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2hmkb_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	Naphthalene 1,2-dioxygenase beta subunit	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
A	d2hmka1	All beta proteins	ISP domain	ISP domain	Ring hydroxylating alpha subunit ISP domain	Naphthalene 1,2-dioxygenase alpha subunit, N-domain	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
A	d2hmka2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	Ring hydroxylating alpha subunit catalytic domain	Naphthalene 1,2-dioxygenase alpha subunit, C-domain	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Ring_hydroxyl_B	e2hmkB1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: Ring_hydroxyl_B	ECOD (1.6)
A	Rieske_5	e2hmkA1	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: Rieske_5	ECOD (1.6)
A	Ring_hydroxyl_A	e2hmkA2	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: Ring_hydroxyl_A	ECOD (1.6)
A	Rieske_1	e2hmkA3	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.2.0)
A	3.90.380.10	Alpha Beta	Alpha-Beta Complex	Naphthalene 1,2-dioxygenase Alpha Subunit	Chain A, domain 1	CATH (4.2.0)
A	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Naphthalene 1,2-dioxygenase beta subunit	oxidoreductase activity catalytic activity dioxygenase activity	cellular response to stimulus catabolic process benzene-containing compound metabolic process response to stimulus oxoacid metabolic process cellular response to xenobiotic stimulus carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus cellular response to chemical stimulus 3-phenylpropionate catabolic process monocarboxylic acid catabolic process cellular response to stimulus catabolic process benzene-containing compound metabolic process response to stimulus oxoacid metabolic process cellular response to xenobiotic stimulus carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus cellular response to chemical stimulus 3-phenylpropionate catabolic process monocarboxylic acid catabolic process response to chemical carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process small molecule catabolic process	-
A	Naphthalene 1,2-dioxygenase alpha subunit	oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen naphthalene 1,2-dioxygenase activity catalytic activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor dioxygenase activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen naphthalene 1,2-dioxygenase activity catalytic activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor dioxygenase activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding	catabolic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
B	IPR000391	Ring-hydroxylating dioxygenase beta subunit	Family
A	IPR017941	Rieske [2Fe-2S] iron-sulphur domain	Domain
A	IPR043266	Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal	Domain
A	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily
A	IPR001663	Aromatic-ring-hydroxylating dioxygenase, alpha subunit	Family
A	IPR015881	Aromatic-ring-hydroxylating dioxygenase ARHD, Rieske 2Fe-2S-binding site	Binding Site
A	IPR015879	Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain	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.