5XBP

Oxygenase component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2

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	d5xbpa1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Diaphorobacter sp. DS2 ) [TaxId: 1302548 ],	SCOPe (2.08)
A	d5xbpa2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	Ring hydroxylating alpha subunit catalytic domain	automated matches	(Diaphorobacter sp. DS2 ) [TaxId: 1302548 ],	SCOPe (2.08)
C [auth D]	d5xbpd1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Diaphorobacter sp. DS2 ) [TaxId: 1302548 ],	SCOPe (2.08)
C [auth D]	d5xbpd2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	Ring hydroxylating alpha subunit catalytic domain	automated matches	(Diaphorobacter sp. DS2 ) [TaxId: 1302548 ],	SCOPe (2.08)
E [auth G]	d5xbpg1	All beta proteins	ISP domain	ISP domain	automated matches	automated matches	(Diaphorobacter sp. DS2 ) [TaxId: 1302548 ],	SCOPe (2.08)
E [auth G]	d5xbpg2	Alpha and beta proteins (a+b)	TBP-like	Bet v1-like	Ring hydroxylating alpha subunit catalytic domain	automated matches	(Diaphorobacter sp. DS2 ) [TaxId: 1302548 ],	SCOPe (2.08)
B [auth C]	d5xbpc_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	automated matches	(Diaphorobacter sp. DS2 ) [TaxId: 1302548 ],	SCOPe (2.08)
D [auth F]	d5xbpf_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	automated matches	(Diaphorobacter sp. DS2 ) [TaxId: 1302548 ],	SCOPe (2.08)
F [auth I]	d5xbpi_	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	Ring hydroxylating beta subunit	automated matches	(Diaphorobacter sp. DS2 ) [TaxId: 1302548 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2 Family	Ring hydroxylating beta subunit-like	8074170	4001024	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	NTF2-like	8074171	3000472	SCOP2 (2022-06-29)
D [auth F]	SCOP2B Superfamily	NTF2-like	8074171	3000472	SCOP2B (2022-06-29)
F [auth I]	SCOP2B Superfamily	NTF2-like	8074171	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	F_UNCLASSIFIED	e5xbpA3	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF00848	e5xbpA2	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: PF00848	ECOD (1.6)
A	PF00355	e5xbpA1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: PF00355	ECOD (1.6)
C [auth D]	F_UNCLASSIFIED	e5xbpD1	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth D]	PF00848	e5xbpD3	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: PF00848	ECOD (1.6)
C [auth D]	PF00355	e5xbpD2	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: PF00355	ECOD (1.6)
E [auth G]	F_UNCLASSIFIED	e5xbpG3	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: F_UNCLASSIFIED	ECOD (1.6)
E [auth G]	PF00848	e5xbpG2	A: a+b two layers	X: TBP-like	H: Bet v1-like (From Topology)	T: Bet v1-like	F: PF00848	ECOD (1.6)
E [auth G]	PF00355	e5xbpG1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: PF00355	ECOD (1.6)
B [auth C]	PF00866	e5xbpC1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: PF00866	ECOD (1.6)
D [auth F]	PF00866	e5xbpF1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: PF00866	ECOD (1.6)
F [auth I]	PF00866	e5xbpI1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: PF00866	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 [auth D]	3.90.380.10	Alpha Beta	Alpha-Beta Complex	Naphthalene 1,2-dioxygenase Alpha Subunit	Chain A, domain 1	CATH (4.3.0)
C [auth D]	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
E [auth G]	3.90.380.10	Alpha Beta	Alpha-Beta Complex	Naphthalene 1,2-dioxygenase Alpha Subunit	Chain A, domain 1	CATH (4.3.0)
E [auth G]	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
B [auth C]	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
D [auth F]	3.10.450.50	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
F [auth I]	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 [auth D], E [auth G]	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 [auth D], E [auth G]	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 [auth C], D [auth F], F [auth I]	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 [auth D], E [auth G]	3NT oxygenase 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	-	-
B [auth C], D [auth F], F [auth I]	3NT oxygenase beta subunit	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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