2B1X | pdb_00002b1x

Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
F	d2b1xf_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	automated matches	automated matches	(Rhodococcus sp. NCIMB 12038 ) [TaxId: 933800 ],	SCOPe (2.08)
D	d2b1xd_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	automated matches	automated matches	(Rhodococcus sp. NCIMB 12038 ) [TaxId: 933800 ],	SCOPe (2.08)
B	d2b1xb1	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	Naphthalene 1,2-dioxygenase beta subunit	(Rhodococcus sp. NCIMB 12038 ) [TaxId: 933800 ],	SCOPe (2.08)
E	d2b1xe1	All beta proteins	ISP domain	ISP domain	Ring hydroxylating alpha subunit ISP domain	Naphthalene 1,2-dioxygenase alpha subunit, N-domain	(Rhodococcus sp. NCIMB 12038 ) [TaxId: 933800 ],	SCOPe (2.08)
E	d2b1xe2	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	(Rhodococcus sp. NCIMB 12038 ) [TaxId: 933800 ],	SCOPe (2.08)
C	d2b1xc1	All beta proteins	ISP domain	ISP domain	Ring hydroxylating alpha subunit ISP domain	Naphthalene 1,2-dioxygenase alpha subunit, N-domain	(Rhodococcus sp. NCIMB 12038 ) [TaxId: 933800 ],	SCOPe (2.08)
C	d2b1xc2	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	(Rhodococcus sp. NCIMB 12038 ) [TaxId: 933800 ],	SCOPe (2.08)
A	d2b1xa1	All beta proteins	ISP domain	ISP domain	Ring hydroxylating alpha subunit ISP domain	Naphthalene 1,2-dioxygenase alpha subunit, N-domain	(Rhodococcus sp. NCIMB 12038 ) [TaxId: 933800 ],	SCOPe (2.08)
A	d2b1xa2	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	(Rhodococcus sp. NCIMB 12038 ) [TaxId: 933800 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	NTF2-like	8037534	3000472	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NTF2-like	8037534	3000472	SCOP2B (2022-06-29)
B	SCOP2 Family	Ring hydroxylating beta subunit-like	8025155	4001024	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	NTF2-like	8037534	3000472	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	Bet v1-like	8037533	3000738	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ISP domain	8037532	3000233	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bet v1-like	8037533	3000738	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ISP domain	8037532	3000233	SCOP2B (2022-06-29)
A	SCOP2 Family	Ring hydroxylating alpha subunit ISP domain	8025153	4001677	SCOP2 (2022-06-29)
A	SCOP2 Family	NdoB catalytic domain-like	8025154	4002055	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ISP domain	8037532	3000233	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Bet v1-like	8037533	3000738	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)
F	Glyco_hydro_18	e2b1xF1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Glyco_hydro_18	ECOD (v294.1)
D	Glyco_hydro_18	e2b1xD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Glyco_hydro_18	ECOD (v294.1)
B	Ring_hydroxyl_B	e2b1xB1	A: a+b two layers	X: Cystatin-like	H: NTF2-like	T: NTF2-like	F: Ring_hydroxyl_B	ECOD (v294.1)
E	Polyketide_cyc2	e2b1xE2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Polyketide_cyc2	ECOD (v294.1)
E	C1_1	e2b1xE3	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: C1_1	ECOD (v294.1)
C	Polyketide_cyc2	e2b1xC2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Polyketide_cyc2	ECOD (v294.1)
C	C1_1	e2b1xC3	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: C1_1	ECOD (v294.1)
A	Ring_hydroxyl_A	e2b1xA2	A: a+b two layers	X: TBP-like	H: Bet v1-like	T: Bet v1-like	F: Ring_hydroxyl_A	ECOD (v294.1)
A	Rieske	e2b1xA3	A: few secondary structure elements	X: Trm112p-like	H: Trm112p-like	T: Trm112p-like	F: Rieske	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
D	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
B	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
E	3.90.380.10	Alpha Beta	Alpha-Beta Complex	Naphthalene 1,2-dioxygenase Alpha Subunit	Chain A, domain 1	CATH (4.3.0)
E	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
C	3.90.380.10	Alpha Beta	Alpha-Beta Complex	Naphthalene 1,2-dioxygenase Alpha Subunit	Chain A, domain 1	CATH (4.3.0)
C	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
A	3.90.380.10	Alpha Beta	Alpha-Beta Complex	Naphthalene 1,2-dioxygenase Alpha Subunit	Chain A, domain 1	CATH (4.3.0)
A	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	naphthalene dioxygenase small 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, C, E	naphthalene dioxygenase large subunit	monooxygenase activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 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 monooxygenase activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 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	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
B, D, F	IPR000391	Ring-hydroxylating dioxygenase beta subunit	Family
A, C, E	IPR017941	Rieske [2Fe-2S] iron-sulphur domain	Domain
A, C, E	IPR043266	Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal	Domain
A, C, E	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily
A, C, E	IPR043257	Ring-hydroxylating dioxygenase large subunit NdoB-related protein, N-terminal Rieske domain	Domain
A, C, E	IPR001663	Aromatic-ring-hydroxylating dioxygenase, alpha subunit	Family
A, C, E	IPR015881	Aromatic-ring-hydroxylating dioxygenase ARHD, Rieske 2Fe-2S-binding site	Binding Site
A, C, E	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.