2XSH

CRYSTAL STRUCTURE OF P4 VARIANT OF BIPHENYL DIOXYGENASE FROM BURKHOLDERIA XENOVORANS LB400 IN COMPLEX WITH 2,6 DI CHLOROBIPHENYL

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	d2xsha1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
A	d2xsha2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
E	d2xshe1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
E	d2xshe2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
C	d2xshc1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
C	d2xshc2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
G	d2xshg1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
G	d2xshg2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
I	d2xshi1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
I	d2xshi2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
K	d2xshk1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
K	d2xshk2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
F	d2xshf_	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	d2xshh_	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	d2xshb_	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	d2xshd_	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	d2xshj_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	automated matches	(Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ],	SCOPe (2.08)
L	d2xshl_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	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)
F	SCOP2B Superfamily	NTF2-like	8074179	3000472	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	NTF2-like	8074179	3000472	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NTF2-like	8074179	3000472	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NTF2-like	8074179	3000472	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	NTF2-like	8074179	3000472	SCOP2B (2022-06-29)
L	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)
A	Rieske_5	e2xshA5	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	e2xshA6	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	e2xshA4	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	e2xshE5	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	e2xshE6	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	e2xshE4	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	e2xshC5	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	e2xshC6	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	e2xshC4	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	e2xshG5	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	e2xshG6	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	e2xshG4	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	e2xshI5	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	e2xshI6	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	e2xshI4	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_1	ECOD (1.6)
K	Rieske_5	e2xshK5	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	e2xshK6	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	e2xshK4	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_1	ECOD (1.6)
F	Ring_hydroxyl_B	e2xshF1	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	e2xshH1	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	e2xshB1	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	e2xshD1	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	e2xshJ1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: Ring_hydroxyl_B	ECOD (1.6)
L	Ring_hydroxyl_B	e2xshL1	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)
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)
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)
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)
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)
F	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)
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)
J	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
L	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, 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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	-
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 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 carboxylic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process cellular response to chemical stimulus response to chemical metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR015881	Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site	Binding Site
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	IPR015879	Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain	Domain
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