2GBX | pdb_00002gbx

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
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)
F	d2gbxf_	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)
B	d2gbxb_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	NTF2-like	8074173	3000472	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NTF2-like	8074173	3000472	SCOP2B (2022-06-29)
B	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)
F	HTHP	e2gbxF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HTHP	ECOD (v294.1)
D	HTHP	e2gbxD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HTHP	ECOD (v294.1)
B	HTHP	e2gbxB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HTHP	ECOD (v294.1)
E		e2gbxE1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)
C		e2gbxC1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)
A		e2gbxA1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 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	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	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.