2BVG

Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 1 (P21)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d2bvga2	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	6-hydroxy-d-nicotine oxidase	automated matches	(Paenarthrobacter nicotinovorans ) [TaxId: 29320 ],	SCOPe (2.08)
A	d2bvga1	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	FAD-linked oxidases, N-terminal domain	automated matches	(Paenarthrobacter nicotinovorans ) [TaxId: 29320 ],	SCOPe (2.08)
B	d2bvgb2	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	6-hydroxy-d-nicotine oxidase	automated matches	(Paenarthrobacter nicotinovorans ) [TaxId: 29320 ],	SCOPe (2.08)
B	d2bvgb1	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	FAD-linked oxidases, N-terminal domain	automated matches	(Paenarthrobacter nicotinovorans ) [TaxId: 29320 ],	SCOPe (2.08)
C	d2bvgc2	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	6-hydroxy-d-nicotine oxidase	automated matches	(Paenarthrobacter nicotinovorans ) [TaxId: 29320 ],	SCOPe (2.08)
C	d2bvgc1	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	FAD-linked oxidases, N-terminal domain	automated matches	(Paenarthrobacter nicotinovorans ) [TaxId: 29320 ],	SCOPe (2.08)
D	d2bvgd2	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	6-hydroxy-d-nicotine oxidase	automated matches	(Paenarthrobacter nicotinovorans ) [TaxId: 29320 ],	SCOPe (2.08)
D	d2bvgd1	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	FAD-linked oxidases, N-terminal domain	automated matches	(Paenarthrobacter nicotinovorans ) [TaxId: 29320 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	BBE	e2bvgA2	A: a+b two layers	X: Alpha-beta plaits	H: FAD-linked oxidases, C-terminal domain (From Topology)	T: FAD-linked oxidases, C-terminal domain	F: BBE	ECOD (1.6)
A	FAD_binding_4	e2bvgA1	A: a+b complex topology	X: FAD-binding domain-like	H: FAD-binding domain (From Topology)	T: FAD-binding domain	F: FAD_binding_4	ECOD (1.6)
B	BBE	e2bvgB2	A: a+b two layers	X: Alpha-beta plaits	H: FAD-linked oxidases, C-terminal domain (From Topology)	T: FAD-linked oxidases, C-terminal domain	F: BBE	ECOD (1.6)
B	FAD_binding_4	e2bvgB1	A: a+b complex topology	X: FAD-binding domain-like	H: FAD-binding domain (From Topology)	T: FAD-binding domain	F: FAD_binding_4	ECOD (1.6)
C	BBE	e2bvgC2	A: a+b two layers	X: Alpha-beta plaits	H: FAD-linked oxidases, C-terminal domain (From Topology)	T: FAD-linked oxidases, C-terminal domain	F: BBE	ECOD (1.6)
C	FAD_binding_4	e2bvgC1	A: a+b complex topology	X: FAD-binding domain-like	H: FAD-binding domain (From Topology)	T: FAD-binding domain	F: FAD_binding_4	ECOD (1.6)
D	BBE	e2bvgD2	A: a+b two layers	X: Alpha-beta plaits	H: FAD-linked oxidases, C-terminal domain (From Topology)	T: FAD-linked oxidases, C-terminal domain	F: BBE	ECOD (1.6)
D	FAD_binding_4	e2bvgD1	A: a+b complex topology	X: FAD-binding domain-like	H: FAD-binding domain (From Topology)	T: FAD-binding domain	F: FAD_binding_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
A	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
A	3.40.462.20	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)
B	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
B	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
B	3.40.462.20	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)
C	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
C	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
C	3.40.462.20	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)
D	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
D	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
D	3.40.462.20	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08031	Berberine and berberine like (BBE)	Berberine and berberine like	This domain is found in the berberine bridge and berberine bridge- like enzymes which are involved in the biosynthesis of numerous isoquinoline alkaloids. They catalyse the transformation of the N-methyl group of (S)-reticuline into the C-8 berberin ...	This domain is found in the berberine bridge and berberine bridge- like enzymes which are involved in the biosynthesis of numerous isoquinoline alkaloids. They catalyse the transformation of the N-methyl group of (S)-reticuline into the C-8 berberine bridge carbon of (S)-scoulerine [1][2].	Domain
A, B, C, D	PF01565	FAD binding domain (FAD_binding_4)	FAD binding domain	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, call ...	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 [1]. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	6-HYDROXY-D-NICOTINE OXIDASE	FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor hydroxy-nicotine oxidase activity oxidoreductase activity, acting on the CH-NH group of donors FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor hydroxy-nicotine oxidase activity oxidoreductase activity, acting on the CH-NH group of donors catalytic activity (R)-6-hydroxynicotine oxidase activity	organonitrogen compound metabolic process organic substance metabolic process nitrogen compound metabolic process alkaloid metabolic process metabolic process nicotine metabolic process catabolic process nicotine catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR016167	FAD-binding, type PCMH, subdomain 1	Homologous Superfamily
A, B, C, D	IPR016164	FAD-linked oxidase-like, C-terminal	Homologous Superfamily
A, B, C, D	IPR006094	FAD linked oxidase, N-terminal	Domain
A, B, C, D	IPR016166	FAD-binding domain, PCMH-type	Domain
A, B, C, D	IPR006093	Oxygen oxidoreductase covalent FAD-binding site	Binding Site
A, B, C, D	IPR012951	Berberine/berberine-like	Domain
A, B, C, D	IPR036318	FAD-binding, type PCMH-like superfamily	Homologous Superfamily
A, B, C, D	IPR016169	FAD-binding, type PCMH, subdomain 2	Homologous Superfamily

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.