URA3/YEL021W Summary Help

Standard Name URA3 1
Systematic Name YEL021W
Feature Type ORF, Verified
Description 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 (1, 2, 3, 4, 5, 6 and see Summary Paragraph)
Name Description URAcil requiring 1, 7
Chromosomal Location
ChrV:116167 to 116970 | ORF Map | GBrowse
Genetic position: -7 cM
Gene Ontology Annotations All URA3 GO evidence and references
  View Computational GO annotations for URA3
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 2 genes
Classical genetics
14 total interaction(s) for 11 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 5
  • Affinity Capture-RNA: 1
  • Co-crystal Structure: 1
  • Two-hybrid: 1

Genetic Interactions
  • Dosage Rescue: 1
  • Synthetic Growth Defect: 3
  • Synthetic Lethality: 2

Expression Summary
Length (a.a.) 267
Molecular Weight (Da) 29,239
Isoelectric Point (pI) 7.37
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrV:116167 to 116970 | ORF Map | GBrowse
Genetic position: -7 cM
Last Update Coordinates: 1996-07-31 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..804 116167..116970 1996-07-31 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000000747

URA3 encodes orotidine 5-phosphate decarboxylase (ODCase), an enzyme involved in the de novo synthesis of pyrimidine ribonucleotides (shown here; 6). ODCase, which is responsible for catalyzing the decarboxylation of orotidine 5-phosphate (OMP) to uridylic acid (UMP), is one of the most proficient enzymes in nature. Not only does it function in the absence of cofactors, ODCase enhances the reaction rate by an unusually large magnitude (1017), reducing a reaction half-time of 78 million years to 18 milliseconds (8, 9, 10, 11). Crystallography experiments and studies of the human and mammalian homologs suggest that the active yeast ODCase functions as a dimer (12 and references contained therein). In mammals, OMP conversion to UMP is mediated by the UMP synthase, which catalyzes both this step in the pathway and the one preceding it (13). S. cerevisiae ODCase shares ~54% sequence similarity with the ODCase domain of the mammalian UMP synthase (11). Mutations in the human homolog UMP synthase lead to the only known human disease of the de novo pyrimidine biosynthetic pathway, orotic aciduria I and II (14).

Loss of ODCase activity leads to a lack of cell growth unless uracil or uridine is added to the media (reviewed in 5). In addition, ODCase can convert 5-FOA into the toxic compound 5-fluorouracil (3). Since URA3 allows for both positive and negative selection, it has been developed as a genetic marker for DNA transformations and other genetic techniques in bacteria and many fungal species (15, 16 and references contained therein).

Uracil starvation or increased levels of the pyrimidine biosynthesis pathway intermediate dihydoorotic acid (DHO) can induce URA3 expression 3-5 fold (1). This regulation is mediated by the transcriptional activator Ppr1p, which binds to the UASURA site (CGGN6CCG) in the promoters of URA1, URA3, and URA4 (17). DNA-bound Ppr1p is transcriptionally inactive, but the addition of DHO converts Ppr1p to an active state that interacts with RNA polymerase II, leading to increased expression of the URA genes (17).

Last updated: 2005-11-17 Contact SGD

References cited on this page View Complete Literature Guide for URA3
1) Lacroute F  (1968) Regulation of pyrimidine biosynthesis in Saccharomyces cerevisiae. J Bacteriol 95(3):824-32
2) Alani E and Kleckner N  (1987) A new type of fusion analysis applicable to many organisms: protein fusions to the URA3 gene of yeast. Genetics 117(1):5-12
3) Boeke JD, et al.  (1984) A positive selection for mutants lacking orotidine-5'-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol Gen Genet 197(2):345-6
4) Boeke JD, et al.  (1987) 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol 154():164-75
5) Jones ME  (1992) Orotidylate decarboxylase of yeast and man. Curr Top Cell Regul 33():331-42
6) Umezu K, et al.  (1971) Purification and properties of orotidine-5'-phosphate pyrophosphorylase and orotidine-5'-phosphate decarboxylase from baker's yeast. J Biochem 70(2):249-62
7) Bach ML, et al.  (1979) Evidence for transcriptional regulation of orotidine-5'-phosphate decarboxylase in yeast by hybridization of mRNA to the yeast structural gene cloned in Escherichia coli. Proc Natl Acad Sci U S A 76(1):386-90
8) Miller BG and Wolfenden R  (2002) Catalytic proficiency: the unusual case of OMP decarboxylase. Annu Rev Biochem 71:847-85
9) Miller BG, et al.  (1999) Activity of yeast orotidine-5'-phosphate decarboxylase in the absence of metals. J Biol Chem 274(34):23841-3
10) Radzicka A and Wolfenden R  (1995) A proficient enzyme. Science 267(5194):90-3
11) Bell JB and Jones ME  (1991) Purification and characterization of yeast orotidine 5'-monophosphate decarboxylase overexpressed from plasmid PGU2. J Biol Chem 266(19):12662-7
12) Miller BG, et al.  (2000) Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog. Proc Natl Acad Sci U S A 97(5):2011-6
13) Langdon SD and Jones ME  (1987) Study of the kinetic and physical properties of the orotidine-5'-monophosphate decarboxylase domain from mouse UMP synthase produced in Saccharomyces cerevisiae. J Biol Chem 262(27):13359-65
14) Floyd EE and Jones ME  (1985) Isolation and characterization of the orotidine 5'-monophosphate decarboxylase domain of the multifunctional protein uridine 5'-monophosphate synthase. J Biol Chem 260(16):9443-51
15) Galvao TC and De Lorenzo V  (2005) Adaptation of the yeast URA3 selection system to gram-negative bacteria and generation of a {delta}betCDE Pseudomonas putida strain. Appl Environ Microbiol 71(2):883-92
16) Francois F, et al.  (2004) Development of an integrative transformation system for the opportunistic pathogenic yeast Candida lusitaniae using URA3 as a selection marker. Yeast 21(2):95-106
17) Flynn PJ and Reece RJ  (1999) Activation of transcription by metabolic intermediates of the pyrimidine biosynthetic pathway. Mol Cell Biol 19(1):882-8