1KRH | pdb_00001krh

X-ray Structure of Benzoate Dioxygenase Reductase

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	d1krha1	All beta proteins	Reductase/isomerase/elongation factor common domain	Riboflavin synthase domain-like	Ferredoxin reductase FAD-binding domain-like	Benzoate dioxygenase reductase	(Acinetobacter sp. ) [TaxId: 472 ],	SCOPe (2.08)
A	d1krha2	Alpha and beta proteins (a/b)	Ferredoxin reductase-like, C-terminal NADP-linked domain	Ferredoxin reductase-like, C-terminal NADP-linked domain	Aromatic dioxygenase reductase-like	Benzoate dioxygenase reductase	(Acinetobacter sp. ) [TaxId: 472 ],	SCOPe (2.08)
A	d1krha3	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Benzoate dioxygenase reductase, N-terminal domain	(Acinetobacter sp. ) [TaxId: 472 ],	SCOPe (2.08)
B	d1krhb1	All beta proteins	Reductase/isomerase/elongation factor common domain	Riboflavin synthase domain-like	Ferredoxin reductase FAD-binding domain-like	Benzoate dioxygenase reductase	(Acinetobacter sp. ) [TaxId: 472 ],	SCOPe (2.08)
B	d1krhb2	Alpha and beta proteins (a/b)	Ferredoxin reductase-like, C-terminal NADP-linked domain	Ferredoxin reductase-like, C-terminal NADP-linked domain	Aromatic dioxygenase reductase-like	Benzoate dioxygenase reductase	(Acinetobacter sp. ) [TaxId: 472 ],	SCOPe (2.08)
B	d1krhb3	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Benzoate dioxygenase reductase, N-terminal domain	(Acinetobacter sp. ) [TaxId: 472 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ferredoxin reductase FAD-binding domain-like	8028205	4002840	SCOP2 (2022-06-29)
A	SCOP2 Family	Aromatic dioxygenase reductase-like	8028207	4003789	SCOP2 (2022-06-29)
A	SCOP2 Family	2Fe-2S ferredoxin domains from multidomain proteins	8028209	4000241	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Riboflavin synthase domain-like	8040584	3001812	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ferredoxin reductase-like, C-terminal NADP-linked domain	8040586	3001461	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	2Fe-2S ferredoxin-like	8040588	3000113	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Riboflavin synthase domain-like	8040584	3001812	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ferredoxin reductase-like, C-terminal NADP-linked domain	8040586	3001461	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8040588	3000113	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	FAD_binding_6	e1krhA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: FAD_binding_6	ECOD (1.6)
A	Fer2	e1krhA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
A	NAD_binding_1	e1krhA3	A: a/b three-layered sandwiches	X: Ferredoxin reductase-like, C-terminal NADP-linked domain (From Topology)	H: Ferredoxin reductase-like, C-terminal NADP-linked domain (From Topology)	T: Ferredoxin reductase-like, C-terminal NADP-linked domain	F: NAD_binding_1	ECOD (1.6)
B	FAD_binding_6	e1krhB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: FAD_binding_6	ECOD (1.6)
B	Fer2	e1krhB2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
B	NAD_binding_1	e1krhB3	A: a/b three-layered sandwiches	X: Ferredoxin reductase-like, C-terminal NADP-linked domain (From Topology)	H: Ferredoxin reductase-like, C-terminal NADP-linked domain (From Topology)	T: Ferredoxin reductase-like, C-terminal NADP-linked domain	F: NAD_binding_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
A	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	3.40.50.80	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module	CATH (4.3.0)
B	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
B	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	3.40.50.80	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00175	Oxidoreductase NAD-binding domain (NAD_binding_1)	Oxidoreductase NAD-binding domain	Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity.	Domain
A, B	PF00111	2Fe-2S iron-sulfur cluster binding domain (Fer2)	2Fe-2S iron-sulfur cluster binding domain		Domain
A, B	PF00970	Oxidoreductase FAD-binding domain (FAD_binding_6)	Oxidoreductase FAD-binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Benzoate 1,2-Dioxygenase Reductase	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding oxidoreductase activity ferredoxin-[NAD(P)H] reductase activity oxidoreductase activity, acting on iron-sulfur proteins as donors oxidoreductase activity, acting on iron-sulfur proteins as donors, NAD or NADP as acceptor ferredoxin-NAD+ reductase activity catalytic activity cation binding ion binding metal ion binding	cellular response to stimulus catabolic process benzene-containing compound metabolic process response to stimulus hydrocarbon catabolic process cellular response to xenobiotic stimulus toluene-containing compound metabolic process xenobiotic catabolic process hydrocarbon metabolic process xenobiotic metabolic process response to xenobiotic stimulus cellular response to chemical stimulus response to chemical toluene catabolic process cellular response to stimulus catabolic process benzene-containing compound metabolic process response to stimulus hydrocarbon catabolic process cellular response to xenobiotic stimulus toluene-containing compound metabolic process xenobiotic catabolic process hydrocarbon metabolic process xenobiotic metabolic process response to xenobiotic stimulus cellular response to chemical stimulus response to chemical toluene catabolic process metabolic process cellular process toluene metabolic process toluene-containing compound catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase	Domain
A, B	IPR001433	Oxidoreductase FAD/NAD(P)-binding	Domain
A, B	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
A, B	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
A, B	IPR006058	2Fe-2S ferredoxin, iron-sulphur binding site	Binding Site
A, B	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain	Homologous Superfamily
A, B	IPR008333	Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain	Domain
A, B	IPR017938	Riboflavin synthase-like beta-barrel	Homologous Superfamily
A, B	IPR017927	FAD-binding domain, ferredoxin reductase-type	Domain
A, B	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, B	IPR047683	Benzoate 1,2-dioxygenase reductase, FAD/NAD binding domain	Domain
A, B	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
A, B	IPR050415	Multicomponent Reductase Electron Transfer	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.