3CYV | pdb_00003cyv

Crystal structure of uroporphyrinogen decarboxylase from Shigella flexineri: new insights into its catalytic mechanism

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	d3cyva_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	UROD/MetE-like	Uroporphyrinogen decarboxylase, UROD	Uroporphyrinogen decarboxylase, UROD	(Shigella flexneri ) [TaxId: 623 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Uroporphyrinogen decarboxylase, UROD	8072668	4003345	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	UROD/MetE-like	8072669	3000657	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)
A	Aldo_ket_red	e3cyvA1	A: alpha bundles	X: Alpha-beta plaits	H: CheC-like	T: CheC-like	F: Aldo_ket_red	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.210	Alpha Beta	Alpha-Beta Barrel	TIM Barrel		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01208	Uroporphyrinogen decarboxylase (URO-D) (URO-D)	Uroporphyrinogen decarboxylase (URO-D)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Uroporphyrinogen decarboxylase	uroporphyrinogen decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process heme biosynthetic process oxoacid metabolic process protoporphyrinogen IX metabolic process pigment biosynthetic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process tetrapyrrole biosynthetic process from glutamate tetrapyrrole biosynthetic process glutamate metabolic process small molecule metabolic process heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process heme biosynthetic process oxoacid metabolic process protoporphyrinogen IX metabolic process pigment biosynthetic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process tetrapyrrole biosynthetic process from glutamate tetrapyrrole biosynthetic process glutamate metabolic process small molecule metabolic process porphyrin-containing compound metabolic process protoporphyrinogen IX biosynthetic process from glutamate tetrapyrrole metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process primary metabolic process protoporphyrinogen IX biosynthetic process biosynthetic process metabolic process cellular process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006361	Uroporphyrinogen decarboxylase HemE	Family
A	IPR038071	UROD/MetE-like superfamily	Homologous Superfamily
A	IPR000257	Uroporphyrinogen decarboxylase (URO-D)	Domain

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.