1SEZ

Crystal Structure of Protoporphyrinogen IX 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)
B	d1sezb1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD-linked reductases, N-terminal domain	Protoporphyrinogen oxidase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
B	d1sezb2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	L-aminoacid/polyamine oxidase	Protoporphyrinogen oxidase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
A	d1seza1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD-linked reductases, N-terminal domain	Protoporphyrinogen oxidase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
A	d1seza2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	L-aminoacid/polyamine oxidase	Protoporphyrinogen oxidase	common tobacco (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Flavoreductase-like	8057750	3000055	SCOP2B (2022-06-29)
A	SCOP2 Family	Amine oxidase-like	8057749	4000128	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Flavoreductase-like	8057750	3000055	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Amino_oxidase_2nd_3	e1sezB1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: Amino_oxidase_2nd_3	ECOD (1.6)
B	Amino_oxidase_1st	e1sezB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Amino_oxidase_1st	ECOD (1.6)
A	Amino_oxidase_2nd_3	e1sezA1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: Amino_oxidase_2nd_3	ECOD (1.6)
A	Amino_oxidase_1st	e1sezA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Amino_oxidase_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
B	3.90.660.20	Alpha Beta	Alpha-Beta Complex	Polyamine Oxidase	Chain A, domain 2	CATH (4.3.0)
B	1.10.3110.10	Mainly Alpha	Orthogonal Bundle	protoporphyrinogen ix oxidase, domain 3	protoporphyrinogen ix oxidase, domain 3	CATH (4.3.0)
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	3.90.660.20	Alpha Beta	Alpha-Beta Complex	Polyamine Oxidase	Chain A, domain 2	CATH (4.3.0)
A	1.10.3110.10	Mainly Alpha	Orthogonal Bundle	protoporphyrinogen ix oxidase, domain 3	protoporphyrinogen ix oxidase, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01593	Flavin containing amine oxidoreductase (Amino_oxidase)	Flavin containing amine oxidoreductase	This family consists of various amine oxidases, including maze polyamine oxidase (PAO) [1] and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene ...	This family consists of various amine oxidases, including maze polyamine oxidase (PAO) [1] and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines [2]. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium [3]. PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines [1]. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Protoporphyrinogen oxidase, mitochondrial	oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors oxygen-dependent protoporphyrinogen oxidase activity catalytic activity oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor protoporphyrinogen oxidase activity	pigment metabolic process heme metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole biosynthetic process tetrapyrrole metabolic process biosynthetic process heme biosynthetic process pigment biosynthetic process metabolic process porphyrin-containing compound metabolic process protoporphyrinogen IX metabolic process protoporphyrinogen IX biosynthetic process	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane cellular anatomical entity intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope mitochondrial envelope organelle cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane cellular anatomical entity intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope mitochondrial envelope organelle cytoplasm organelle membrane plastid chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002937	Amine oxidase	Domain
A, B	IPR050464	Zeta Carotene Desaturase and Related Oxidoreductases	Family
A, B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR004572	Protoporphyrinogen oxidase	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.