1ULJ

Biphenyl dioxygenase (BphA1A2) in complex with the substrate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
A	d1ulja1	All beta proteins	ISP domain	ISP domain	Ring hydroxylating alpha subunit ISP domain	Biphenyl dioxygenase large subunit BphA1, N-terminal domain	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
A	d1ulja2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	Ring hydroxylating alpha subunit catalytic domain	Biphenyl dioxygenase large subunit BphA1, C-terminal domain	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
C	d1uljc1	All beta proteins	ISP domain	ISP domain	Ring hydroxylating alpha subunit ISP domain	Biphenyl dioxygenase large subunit BphA1, N-terminal domain	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
C	d1uljc2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	Ring hydroxylating alpha subunit catalytic domain	Biphenyl dioxygenase large subunit BphA1, C-terminal domain	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
E	d1ulje1	All beta proteins	ISP domain	ISP domain	Ring hydroxylating alpha subunit ISP domain	Biphenyl dioxygenase large subunit BphA1, N-terminal domain	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
E	d1ulje2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	Ring hydroxylating alpha subunit catalytic domain	Biphenyl dioxygenase large subunit BphA1, C-terminal domain	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
B	d1uljb_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	Biphenyl dioxygenase small subunit BphA2	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
D	d1uljd_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	Biphenyl dioxygenase small subunit BphA2	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
F	d1uljf_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	Biphenyl dioxygenase small subunit BphA2	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Bet v1-like	8040912	3000738	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ISP domain	8040910	3000233	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bet v1-like	8040912	3000738	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ISP domain	8040910	3000233	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ISP domain	8040910	3000233	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Bet v1-like	8040912	3000738	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NTF2-like	8040914	3000472	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NTF2-like	8040914	3000472	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	NTF2-like	8040914	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	Rieske_5	e1uljA1	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	e1uljA2	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	e1uljA3	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_1	ECOD (1.6)
C	Rieske_5	e1uljC1	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: Rieske_5	ECOD (1.6)
C	Ring_hydroxyl_A	e1uljC2	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)
C	Rieske_1	e1uljC3	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_1	ECOD (1.6)
E	Rieske_5	e1uljE1	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: Rieske_5	ECOD (1.6)
E	Ring_hydroxyl_A	e1uljE2	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)
E	Rieske_1	e1uljE3	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_1	ECOD (1.6)
B	Ring_hydroxyl_B	e1uljB1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: Ring_hydroxyl_B	ECOD (1.6)
D	Ring_hydroxyl_B	e1uljD1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: Ring_hydroxyl_B	ECOD (1.6)
F	Ring_hydroxyl_B	e1uljF1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: Ring_hydroxyl_B	ECOD (1.6)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF00848	Ring hydroxylating alpha subunit (catalytic domain) (Ring_hydroxyl_A)	Ring hydroxylating alpha subunit (catalytic domain)	This family is the catalytic domain of aromatic-ring- hydroxylating dioxygenase systems. The active site contains a non-heme ferrous ion coordinated by three ligands.	Domain
A, C, E	PF00355	Rieske [2Fe-2S] domain (Rieske)	Rieske [2Fe-2S] domain	The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in ...	The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilises the protein [4].	Domain
B, D, F	PF00866	Ring hydroxylating beta subunit (Ring_hydroxyl_B)	Ring hydroxylating beta subunit	This subunit has a similar structure to NTF-2 and scytalone dehydratase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	biphenyl dioxygenase large subunit	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding biphenyl 2,3-dioxygenase activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 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 cation binding transition metal ion binding iron ion binding iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding biphenyl 2,3-dioxygenase activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 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 cation binding transition metal ion binding iron ion binding ion binding metal ion binding	catabolic process metabolic process	-
B, D, F	biphenyl dioxygenase small subunit	biphenyl 2,3-dioxygenase activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 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	cellular response to stimulus catabolic process response to stimulus oxoacid metabolic process organic acid metabolic process organic acid catabolic process response to xenobiotic stimulus cellular catabolic process 3-phenylpropionate catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process 3-phenylpropionate metabolic process benzene-containing compound metabolic process cellular response to stimulus catabolic process response to stimulus oxoacid metabolic process organic acid metabolic process organic acid catabolic process response to xenobiotic stimulus cellular catabolic process 3-phenylpropionate catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process 3-phenylpropionate metabolic process benzene-containing compound metabolic process cellular response to xenobiotic stimulus cellular metabolic process carboxylic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process cellular response to chemical stimulus response to chemical cellular process 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	IPR015881	Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site	Binding Site
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	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

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.