2YFI | pdb_00002yfi

Crystal Structure of Biphenyl dioxygenase variant RR41 (BPDO-RR41)

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)
L	d2yfil_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
J	d2yfij_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
H	d2yfih_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
F	d2yfif_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
D	d2yfid_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
B	d2yfib_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
K	d2yfik1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
K	d2yfik2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
I	d2yfii1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
I	d2yfii2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
G	d2yfig1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
G	d2yfig2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
E	d2yfie1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
E	d2yfie2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
C	d2yfic1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
C	d2yfic2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
A	d2yfia1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
A	d2yfia2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	NTF2-like	8074179	3000472	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	NTF2-like	8074179	3000472	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	NTF2-like	8074179	3000472	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	NTF2-like	8074179	3000472	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NTF2-like	8074179	3000472	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NTF2-like	8074179	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)
L	Ring_hydroxyl_B	e2yfiL1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: Ring_hydroxyl_B	ECOD (1.6)
J	Ring_hydroxyl_B	e2yfiJ1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: Ring_hydroxyl_B	ECOD (1.6)
H	Ring_hydroxyl_B	e2yfiH1	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	e2yfiF1	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	e2yfiD1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: Ring_hydroxyl_B	ECOD (1.6)
B	Ring_hydroxyl_B	e2yfiB1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: Ring_hydroxyl_B	ECOD (1.6)
K	Rieske_5	e2yfiK5	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: Rieske_5	ECOD (1.6)
K	Ring_hydroxyl_A	e2yfiK6	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)
K	Rieske_1	e2yfiK2	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_1	ECOD (1.6)
I	Rieske_5	e2yfiI5	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: Rieske_5	ECOD (1.6)
I	Ring_hydroxyl_A	e2yfiI6	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)
I	Rieske_1	e2yfiI2	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_1	ECOD (1.6)
G	Rieske_5	e2yfiG8	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: Rieske_5	ECOD (1.6)
G	Ring_hydroxyl_A	e2yfiG9	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)
G	Rieske_1	e2yfiG7	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	e2yfiE8	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	e2yfiE9	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	e2yfiE7	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	e2yfiC8	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	e2yfiC9	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	e2yfiC7	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_1	ECOD (1.6)
A	Rieske_5	e2yfiA8	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	e2yfiA9	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	e2yfiA7	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)
L	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
J	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
H	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)
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)
K	3.90.380.10	Alpha Beta	Alpha-Beta Complex	Naphthalene 1,2-dioxygenase Alpha Subunit	Chain A, domain 1	CATH (4.3.0)
K	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
I	3.90.380.10	Alpha Beta	Alpha-Beta Complex	Naphthalene 1,2-dioxygenase Alpha Subunit	Chain A, domain 1	CATH (4.3.0)
I	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
G	3.90.380.10	Alpha Beta	Alpha-Beta Complex	Naphthalene 1,2-dioxygenase Alpha Subunit	Chain A, domain 1	CATH (4.3.0)
G	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L	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
A, C, E, G, I A, C, E, G, I, K	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, G, I A, C, E, G, I, K	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L	BIPHENYL DIOXYGENASE SUBUNIT BETA	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 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, G, I A, C, E, G, I, K	BIPHENYL DIOXYGENASE SUBUNIT ALPHA	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 cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

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