2YVJ

Crystal structure of the ferredoxin-ferredoxin reductase (BPHA3-BPHA4)complex

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	d2yvja2	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD/NAD-linked reductases, N-terminal and central domains	NADH-dependent ferredoxin reductase, BphA4, middle domain	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
A	d2yvja1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD/NAD-linked reductases, N-terminal and central domains	NADH-dependent ferredoxin reductase, BphA4, N- and C-terminal domain	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
A	d2yvja3	Alpha and beta proteins (a+b)	CO dehydrogenase flavoprotein C-domain-like	FAD/NAD-linked reductases, dimerisation (C-terminal) domain	FAD/NAD-linked reductases, dimerisation (C-terminal) domain	NADH-dependent ferredoxin reductase, BphA4	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
A	d2yvja4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
C [auth P]	d2yvjp2	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD/NAD-linked reductases, N-terminal and central domains	NADH-dependent ferredoxin reductase, BphA4, middle domain	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
C [auth P]	d2yvjp1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD/NAD-linked reductases, N-terminal and central domains	NADH-dependent ferredoxin reductase, BphA4, N- and C-terminal domain	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
C [auth P]	d2yvjp3	Alpha and beta proteins (a+b)	CO dehydrogenase flavoprotein C-domain-like	FAD/NAD-linked reductases, dimerisation (C-terminal) domain	FAD/NAD-linked reductases, dimerisation (C-terminal) domain	NADH-dependent ferredoxin reductase, BphA4	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
C [auth P]	d2yvjp4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)
B	d2yvjb_	All beta proteins	ISP domain	ISP domain	Rieske iron-sulfur protein (ISP)	automated matches	(Pseudomonas sp. ) [TaxId: 306 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Thioredoxin reductase-like	8056220	3000050	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GSR C-terminal domain-like	8056221	3000028	SCOP2B (2022-06-29)
C [auth P]	SCOP2B Superfamily	GSR C-terminal domain-like	8056221	3000028	SCOP2B (2022-06-29)
C [auth P]	SCOP2B Superfamily	Thioredoxin reductase-like	8056220	3000050	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ISP domain	8080526	3000233	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	Reductase_C	e2yvjA1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: Reductase_C	ECOD (1.6)
A	Pyr_redox_2_1	e2yvjA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_1	ECOD (1.6)
A	Pyr_redox_2	e2yvjA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)
C [auth P]	Reductase_C	e2yvjP1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: Reductase_C	ECOD (1.6)
C [auth P]	Pyr_redox_2_1	e2yvjP3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_1	ECOD (1.6)
C [auth P]	Pyr_redox_2	e2yvjP2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)
B	Rieske_3	e2yvjB1	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: Rieske_3	ECOD (1.6)
B	Rieske_1	e2yvjB2	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
C [auth P]	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
C [auth P]	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
B	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth P]	PF07992	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain
A, C [auth P]	PF14759	Reductase C-terminal (Reductase_C)	Reductase C-terminal	This domain occurs at the C-terminus of various reductase enzymes, including putidaredoxin reductase, ferredoxin reductase, 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin--NAD(+) reductase component, benzene 1,2-dioxygenase system ferredoxin ...	This domain occurs at the C-terminus of various reductase enzymes, including putidaredoxin reductase, ferredoxin reductase, 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin--NAD(+) reductase component, benzene 1,2-dioxygenase system ferredoxin--NAD(+) reductase subunit, rhodocoxin reductase, biphenyl dioxygenase system ferredoxin--NAD(+) reductase component, rubredoxin-NAD(+) reductase and toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component. In putidaredoxin reductase this domain is involved in dimerisation [1]. In the FAD-containing NADH-ferredoxin reductase (BphA4) it is responsible for interaction with the Rieske-type [2Fe-2S] ferredoxin (BphA3) [2].	Domain
B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth P]	Ferredoxin reductase	oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm
B	Biphenyl dioxygenase ferredoxin subunit	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	catabolic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth P]	IPR028202	Reductase, C-terminal	Domain
A, C [auth P]	IPR023753	FAD/NAD(P)-binding domain	Domain
A, C [auth P]	IPR016156	FAD/NAD-linked reductase, dimerisation domain superfamily	Homologous Superfamily
A, C [auth P]	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, C [auth P]	IPR050446	FAD-dependent Oxidoreductases and Apoptosis Regulators	Family
B	IPR017941	Rieske [2Fe-2S] iron-sulphur domain	Domain
B	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily

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.