2IVE | pdb_00002ive

Structure of protoporphyrinogen oxidase from Myxococcus xanthus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d2ivea1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD-linked reductases, N-terminal domain	Protoporphyrinogen oxidase	(Myxococcus xanthus ) [TaxId: 34 ],	SCOPe (2.08)
A	d2ivea2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	L-aminoacid/polyamine oxidase	Protoporphyrinogen oxidase	(Myxococcus xanthus ) [TaxId: 34 ],	SCOPe (2.08)
B	d2iveb1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD-linked reductases, N-terminal domain	Protoporphyrinogen oxidase	(Myxococcus xanthus ) [TaxId: 34 ],	SCOPe (2.08)
B	d2iveb2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	L-aminoacid/polyamine oxidase	Protoporphyrinogen oxidase	(Myxococcus xanthus ) [TaxId: 34 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Flavoreductase-like	8057753	3000055	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Flavoreductase-like	8057753	3000055	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	YceM-like_C	e2iveA1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
A	NAD_binding_8	e2iveA2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_8	ECOD (develop294)
B	YceM-like_C	e2iveB1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
B	NAD_binding_8	e2iveB2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_8	ECOD (develop294)

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	3.90.660.20	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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PROTOPORPHYRINOGEN OXIDASE	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	heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process heme biosynthetic process protoporphyrinogen IX metabolic process pigment biosynthetic process protoporphyrinogen IX biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.