1NDO | pdb_00001ndo

NAPHTHALENE 1,2-DIOXYGENASE

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ndoa1	All beta proteins	ISP domain	ISP domain	Ring hydroxylating alpha subunit ISP domain	Naphthalene 1,2-dioxygenase alpha subunit, N-domain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
A	d1ndoa2	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 putida ) [TaxId: 303 ],	SCOPe (2.08)
C	d1ndoc1	All beta proteins	ISP domain	ISP domain	Ring hydroxylating alpha subunit ISP domain	Naphthalene 1,2-dioxygenase alpha subunit, N-domain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
C	d1ndoc2	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 putida ) [TaxId: 303 ],	SCOPe (2.08)
E	d1ndoe1	All beta proteins	ISP domain	ISP domain	Ring hydroxylating alpha subunit ISP domain	Naphthalene 1,2-dioxygenase alpha subunit, N-domain	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
E	d1ndoe2	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 putida ) [TaxId: 303 ],	SCOPe (2.08)
B	d1ndob_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	Naphthalene 1,2-dioxygenase beta subunit	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
D	d1ndod_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	Naphthalene 1,2-dioxygenase beta subunit	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
F	d1ndof_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	Naphthalene 1,2-dioxygenase beta subunit	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	ISP domain	8044085	3000233	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bet v1-like	8044087	3000738	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ISP domain	8044085	3000233	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bet v1-like	8044087	3000738	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Bet v1-like	8044087	3000738	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ISP domain	8044085	3000233	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NTF2-like	8044088	3000472	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NTF2-like	8044088	3000472	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	NTF2-like	8044088	3000472	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)
A		e1ndoA1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Urease_alpha	F:	ECOD (20:10:01)
A		e1ndoA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
A		e1ndoA3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: EGF_CA	F:	ECOD (20:10:01)
C		e1ndoC1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Urease_alpha	F:	ECOD (20:10:01)
C		e1ndoC2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
C		e1ndoC3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: EGF_CA	F:	ECOD (20:10:01)
E		e1ndoE1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Urease_alpha	F:	ECOD (20:10:01)
E		e1ndoE2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
E		e1ndoE3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: EGF_CA	F:	ECOD (20:10:01)
B		e1ndoB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
D		e1ndoD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
F		e1ndoF1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
B	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)
F	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	NAPHTHALENE 1,2-DIOXYGENASE	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	-	-
B, D, F	NAPHTHALENE 1,2-DIOXYGENASE	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	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
B, D, F	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
B, D, F	IPR000391	Ring-hydroxylating dioxygenase beta subunit	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, E	naphthalene 1,2-dioxygenase M-CSA #130	The naphthalene dioxygenase (NDO) multicomponent enzyme system catalyses the incorporation of both atoms of molecular oxygen into naphthalene to form cis-naphthalene dihydrodiol. The enzyme comprises an NADH binding reductase, a Rieske feredoxin, and a oxygenase component. All three units contain [2Fe-2S] clusters. NDO is a member of the ring-hydroxylating dioxygenase (RHD) family of bacterial enzymes that play a critical role in the degradation of aromatic compounds.	Defined by 5 residues: HIS:A-104ASP:E-205HIS:E-208HIS:E-213ASP:E-362 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.14.12.12 (PDB Primary Data) Search M-CSA Motif + EC 1.14.12.12

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.