URA3 orotidine-5'-phosphate decarboxylase [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: URA3
Official Full Name: orotidine-5'-phosphate decarboxylase
Primary source: SGD:S000000747
Locus tag: YEL021W
See related: AllianceGenome:SGD:S000000747; FungiDB:YEL021W; VEuPathDB:YEL021W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables orotidine-5'-phosphate decarboxylase activity. Involved in 'de novo' pyrimidine nucleobase biosynthetic process and UMP biosynthetic process. Located in cytosol. Human ortholog(s) of this gene implicated in orotic aciduria and purine-pyrimidine metabolic disorder. Orthologous to human UMPS (uridine monophosphate synthetase). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See URA3 in Genome Data Viewer

Location:: chromosome: V

Exon count:: 1

Sequence:: Chromosome: V; NC_001137.3 (116167..116970)

Chromosome V - NC_001137.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001137.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

[URA3 affects artemisinic acid production by an engineered Saccharomyces cerevisiae in pilot-scale fermentation].
Title: [URA3 affects artemisinic acid production by an engineered Saccharomyces cerevisiae in pilot-scale fermentation].
Repetitive delta-integration of a cellulase-encoding gene into the chromosome of an industrial Angel Yeast-derived strain by URA3 recycling.
Title: Repetitive δ-integration of a cellulase-encoding gene into the chromosome of an industrial Angel Yeast-derived strain by URA3 recycling.
SIR2 Expression Noise Can Generate Heterogeneity in Viability but Does Not Affect Cell-to-Cell Epigenetic Silencing of Subtelomeric URA3 in Yeast.
Title: SIR2 Expression Noise Can Generate Heterogeneity in Viability but Does Not Affect Cell-to-Cell Epigenetic Silencing of Subtelomeric URA3 in Yeast.
Role of the Carboxylate in Enzyme-Catalyzed Decarboxylation of Orotidine 5'-Monophosphate: Transition State Stabilization Dominates Over Ground State Destabilization.
Title: Role of the Carboxylate in Enzyme-Catalyzed Decarboxylation of Orotidine 5'-Monophosphate: Transition State Stabilization Dominates Over Ground State Destabilization.
most of the compensatory mutants were clustered in proximity to the catalytic center
Title: Limits to Compensatory Mutations: Insights from Temperature-Sensitive Alleles.
Heritable silencing does not impact mutation rate but drives population size expansion and rapid epigenetic adaptation. This eventually leads to genetic assimilation of the silent phenotype by mutations that reduce or abolish URA3 expression.
Title: Epigenetic gene silencing alters the mechanisms and rate of evolutionary adaptation.
we showed that high levels of copper (previously shown to elevate CUP1 transcription) lead to a substantial elevation in rate of both interhomolog and intra/sister chromatid recombination in the CUP1 array; recombination events that delete the URA3 insertion from the CUP1 array occur at a rate of >10(-3)/division in unselected cells.
Title: Properties of Mitotic and Meiotic Recombination in the Tandemly-Repeated CUP1 Gene Cluster in the Yeast Saccharomyces cerevisiae.
We found that mutations were scattered throughout the open reading frame of the URA3 gene but clustered to several hotspots with base substitutions/deletions at homo-polymeric runs. Surprisingly, we only detected two multiple mutants out of over 300 sequenced mutation events.
Title: Microhomology-mediated end joining induces hypermutagenesis at breakpoint junctions.
Analysis of a triple mutant cube shows small interactions between phosphodianion gripper side chains, which are consistent with steric crowding of the side chains around the phosphodianion at wild-type OMPDC
Title: Enzyme architecture: deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5'-monophosphate decarboxylase.
investigation of OMPDC/URA3 biocatalysis: substrate specificity; kinetics; conformational changes during substrate binding/decarboxylation
Title: Catalysis by orotidine 5'-monophosphate decarboxylase: effect of 5-fluoro and 4'-substituents on the decarboxylation of two-part substrates.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D17S1248 (e-PCR)
- UniSTS:149861

Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables carboxy-lyase activity	IEA Inferred from Electronic Annotation more info
enables orotidine-5'-phosphate decarboxylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables orotidine-5'-phosphate decarboxylase activity	IDA Inferred from Direct Assay more info	PubMed
enables orotidine-5'-phosphate decarboxylase activity	IEA Inferred from Electronic Annotation more info
enables orotidine-5'-phosphate decarboxylase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in 'de novo' UMP biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in 'de novo' pyrimidine nucleobase biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in 'de novo' pyrimidine nucleobase biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in 'de novo' pyrimidine nucleobase biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in UMP biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in UMP biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleobase-containing small molecule metabolic process	IEA Inferred from Electronic Annotation more info
involved_in pyrimidine nucleotide biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in pyrimidine-containing compound biosynthetic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: orotidine-5'-phosphate decarboxylase

NP_010893.3

EC 4.1.1.23

Orotidine-5'-phosphate (OMP) decarboxylase; catalyzes the sixth enzymatic step in the de novo biosynthesis of pyrimidines, converting OMP into uridine monophosphate (UMP); converts 5-FOA into 5-fluorouracil, a toxic compound

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001137.3 Reference assembly

Range

116167..116970

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001178836.3 → NP_010893.3 TPA: orotidine-5'-phosphate decarboxylase [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010893.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D3DLM7, P03962

UniProtKB/TrEMBL

A6ZQS7, B5VHB5, C7GX21, C8Z6X5, G2WCL0, N1P5L4

Conserved Domains (1) summary

cl21457
Location:32 → 252

TIM; TIM-like beta/alpha barrel domains