3GZX

Crystal Structure of the Biphenyl Dioxygenase in complex with Biphenyl from Comamonas testosteroni Sp. Strain B-356

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3gzxa1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	Pseudomonas testosteroni (Comamonas testosteroni ) [TaxId: 285 ],	SCOPe (2.08)
A	d3gzxa2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	automated matches	automated matches	Pseudomonas testosteroni (Comamonas testosteroni ) [TaxId: 285 ],	SCOPe (2.08)
B	d3gzxb_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	automated matches	Pseudomonas testosteroni (Comamonas testosteroni ) [TaxId: 285 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Ring hydroxylating beta subunit-like	8074176	4001024	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	NTF2-like	8074177	3000472	SCOP2 (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	e3gzxA5	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	e3gzxA2	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	e3gzxA4	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	e3gzxB1	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)
B	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	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	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	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	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	-	-
B	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	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.