5MXJ

Structure of the Y108F mutant of vanillyl alcohol oxidase

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	d5mxja2	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	Vanillyl-alcohol oxidase-like	automated matches	(Penicillium simplicissimum ) [TaxId: 69488 ],	SCOPe (2.08)
A	d5mxja1	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	(Penicillium simplicissimum ) [TaxId: 69488 ],	SCOPe (2.08)
B	d5mxjb2	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	Vanillyl-alcohol oxidase-like	automated matches	(Penicillium simplicissimum ) [TaxId: 69488 ],	SCOPe (2.08)
B	d5mxjb1	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	(Penicillium simplicissimum ) [TaxId: 69488 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FAD-binding/transporter-associated domain-like	8036676	3000913	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FAD-linked oxidases C-terminal domain-like	8035624	3001317	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FAD-binding/transporter-associated domain-like	8036676	3000913	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FAD-linked oxidases C-terminal domain-like	8035624	3001317	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-oxidase_C	e5mxjA2	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: FAD-oxidase_C	ECOD (1.6)
A	FAD_binding_4	e5mxjA1	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	FAD-oxidase_C	e5mxjB2	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: FAD-oxidase_C	ECOD (1.6)
B	FAD_binding_4	e5mxjB1	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	3.40.462.10	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)
A	1.10.45.10	Mainly Alpha	Orthogonal Bundle	Vanillyl-alcohol Oxidase	Chain A, domain 4	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	3.40.462.10	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)
B	1.10.45.10	Mainly Alpha	Orthogonal Bundle	Vanillyl-alcohol Oxidase	Chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02913	FAD linked oxidases, C-terminal domain (FAD-oxidase_C)	FAD linked oxidases, C-terminal domain	This domain has a ferredoxin-like fold.	Domain
A, B	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	Vanillyl-alcohol oxidase	oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors lactate dehydrogenase activity D-lactate dehydrogenase activity catalytic activity D-lactate dehydrogenase (cytochrome) activity oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors lactate dehydrogenase activity D-lactate dehydrogenase activity catalytic activity D-lactate dehydrogenase (cytochrome) activity oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor 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, acting on the CH-OH group of donors, oxygen as acceptor vanillyl-alcohol oxidase activity	catabolic process oxoacid metabolic process lactate catabolic process organic hydroxy compound metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process lactate metabolic process cellular catabolic process monocarboxylic acid catabolic process organic hydroxy compound catabolic process carboxylic acid catabolic process metabolic process cellular process catabolic process oxoacid metabolic process lactate catabolic process organic hydroxy compound metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process lactate metabolic process cellular catabolic process monocarboxylic acid catabolic process organic hydroxy compound catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process small molecule catabolic process alcohol metabolic process methanol metabolic process primary alcohol metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle peroxisome microbody

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016167	FAD-binding, type PCMH, subdomain 1	Homologous Superfamily
A, B	IPR016164	FAD-linked oxidase-like, C-terminal	Homologous Superfamily
A, B	IPR016170	Cytokinin dehydrogenase, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR006094	FAD linked oxidase, N-terminal	Domain
A, B	IPR004113	FAD-binding oxidoreductase/transferase, type 4, C-terminal	Domain
A, B	IPR016166	FAD-binding domain, PCMH-type	Domain
A, B	IPR016171	Vanillyl-alcohol oxidase, C-terminal subdomain 2	Homologous Superfamily
A, B	IPR036318	FAD-binding, type PCMH-like superfamily	Homologous Superfamily
A, B	IPR016169	FAD-binding, type PCMH, subdomain 2	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.