2GBX

Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1 Bound to Biphenyl

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	d2gbxa1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Sphingobium yanoikuyae ) [TaxId: 13690 ],	SCOPe (2.08)
A	d2gbxa2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Sphingobium yanoikuyae ) [TaxId: 13690 ],	SCOPe (2.08)
C	d2gbxc1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Sphingobium yanoikuyae ) [TaxId: 13690 ],	SCOPe (2.08)
C	d2gbxc2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Sphingobium yanoikuyae ) [TaxId: 13690 ],	SCOPe (2.08)
E	d2gbxe1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Sphingobium yanoikuyae ) [TaxId: 13690 ],	SCOPe (2.08)
E	d2gbxe2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	(Sphingobium yanoikuyae ) [TaxId: 13690 ],	SCOPe (2.08)
B	d2gbxb_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	automated matches	automated matches	(Sphingobium yanoikuyae ) [TaxId: 13690 ],	SCOPe (2.08)
D	d2gbxd_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	automated matches	automated matches	(Sphingobium yanoikuyae ) [TaxId: 13690 ],	SCOPe (2.08)
F	d2gbxf_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	automated matches	automated matches	(Sphingobium yanoikuyae ) [TaxId: 13690 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	NTF2-like	8074173	3000472	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NTF2-like	8074173	3000472	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	NTF2-like	8074173	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	e2gbxA4	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	e2gbxA3	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	e2gbxA1	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	e2gbxC2	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	e2gbxC1	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	e2gbxC3	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	e2gbxE3	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	e2gbxE1	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	e2gbxE2	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	e2gbxB1	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	e2gbxD1	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	e2gbxF1	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 2,3-Dioxygenase Alpha Subunit	oxidoreductase activity catalytic activity 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	catabolic process metabolic process cellular process	-
B, D, F	Biphenyl 2,3-Dioxygenase Beta Subunit	oxidoreductase activity catalytic activity dioxygenase activity cation binding ion binding binding metal ion binding small molecule binding	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	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.