1DBT

CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH UMP

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1dbta_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1dbtb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1dbtc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase)	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Decarboxylase	8030861	4003062	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribulose-phoshate binding barrel	8043240	3000216	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043240	3000216	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043240	3000216	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	OMPdecase	e1dbtA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: OMPdecase	ECOD (1.6)
B	OMPdecase	e1dbtB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: OMPdecase	ECOD (1.6)
C	OMPdecase	e1dbtC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: OMPdecase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00215	Orotidine 5'-phosphate decarboxylase / HUMPS family (OMPdecase)	Orotidine 5'-phosphate decarboxylase / HUMPS family	This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly ...	This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly related to Pfam:PF00834.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	OROTIDINE 5'-PHOSPHATE DECARBOXYLASE	orotidine-5'-phosphate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	organonitrogen compound metabolic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process organonitrogen compound biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process organonitrogen compound metabolic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process organonitrogen compound biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process 'de novo' pyrimidine nucleobase biosynthetic process small molecule metabolic process metabolic process pyrimidine-containing compound biosynthetic process ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process 'de novo' UMP biosynthetic process ribonucleotide biosynthetic process UMP biosynthetic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process phosphate-containing compound metabolic process UMP metabolic process phosphorus metabolic process nucleoside monophosphate metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process cellular metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process cellular process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR018089	Orotidine 5'-phosphate decarboxylase, active site	Active Site
A, B, C	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A, B, C	IPR047596	Orotidine 5'-phosphate decarboxylase, bacterial	Family
A, B, C	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C	IPR001754	Orotidine 5'-phosphate decarboxylase domain	Domain
A, B, C	IPR014732	Orotidine 5'-phosphate decarboxylase	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, B	orotidine-5'-phosphate decarboxylase M-CSA #50	Orotidine-5'-phosphate decarboxylase catalyses the decarboxylation of orotidine-5'-phosphate, the sixth and final step in the de novo pyrimidine biosynthesis of uridine monophosphate. It accelerates the reaction by 10^17 and hence is the most proficient enzyme discovered so far. In most prokaryotes the bioactive form is a homodimer. In higher organisms it is part of a bifunctional enzyme.	Defined by 6 residues: LYS:A-33ASP:A-60LYS:A-62THR:A-123ARG:A-215ASP:B-65 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.1.23 (PDB Primary Data) Search M-CSA Motif + EC 4.1.1.23

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.