4.1.1.23: orotidine-5'-phosphate decarboxylase
This is an abbreviated version!
For detailed information about orotidine-5'-phosphate decarboxylase, go to the full flat file.
Word Map on EC 4.1.1.23
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4.1.1.23
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pyrimidine
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phosphoribosyltransferase
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uracil
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auxotrophic
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dihydroorotase
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5-fluoroorotic
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2.4.2.10
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phosphoribosyl
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6-azauridine
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pyrazofurin
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transcarbamoylase
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carbanions
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oprtase
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aciduria
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5-fluorouridine
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dianion
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prototrophy
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barbituric
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succinate-grown
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phosphite
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phosphodianion
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pyre
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molecular biology
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pharmacology
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medicine
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biotechnology
- 4.1.1.23
- pyrimidine
-
phosphoribosyltransferase
- uracil
-
auxotrophic
- dihydroorotase
-
5-fluoroorotic
-
2.4.2.10
-
phosphoribosyl
- 6-azauridine
- pyrazofurin
-
transcarbamoylase
-
carbanions
- oprtase
-
aciduria
- 5-fluorouridine
- dianion
-
prototrophy
-
barbituric
-
succinate-grown
- phosphite
-
phosphodianion
-
pyre
- molecular biology
- pharmacology
- medicine
- biotechnology
Reaction
Synonyms
Decarboxylase, orotidine 5'-phosphate, More, ODCase, OMP decarboxylase, OMP-DC, OMPD, OMPDC, OMPDCase, OMPdecase, Orotate decarboxylase, Orotate monophosphate decarboxylase, Orotic decarboxylase, Orotidine 5'-monophosphate decarboxylase, Orotidine 5'-phosphate decarboxylase, orotidine 5-monophosphate decarboxylase, orotidine 5-phosphate decarboxylase, Orotidine monophosphate decarboxylase, Orotidine phosphate decarboxylase, Orotidine-5'-monophosphate decarboxylase, orotidine-5'-phosphate decarboxylase, orotidine-5-monophosphate decarboxylase, Orotidylate decarboxylase, Orotidylic acid decarboxylase, Orotidylic decarboxylase, Orotodylate decarboxylase, PbrURA3, PfODCase, PfOMPDC, pm-ura3, PyrF, ScOMPDC, UMP synthase, URA3, Uridine 5'-monophosphate synthase
ECTree
4.1.1.23 orotidine-5'-phosphate decarboxylaseAdvanced search results
results (
results (Engineering
Engineering on EC 4.1.1.23 - orotidine-5'-phosphate decarboxylase
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PROTEIN VARIANTS 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
D70N
Methanobacterium thermoautotrophicus DSM 1053
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0.002% of wild-type activity
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I96S
Methanobacterium thermoautotrophicus DSM 1053
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0.5% of wild-type activity
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I96T
Methanobacterium thermoautotrophicus DSM 1053
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15% of wild-type activity
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L123N
Methanobacterium thermoautotrophicus DSM 1053
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10% of wild-type activity
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D70A
D70A/K72A
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active site double mutant, markedly less stable than native enzyme
D70G
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active site mutant, markedly less stable than native enzyme
D75N
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mutation of an active site residue contributed by the other monomer in the active dimer
Q185A
R160A/V182A
1700fold decrease in catalytic efficiency
R160A/Y206F
R203A
1900fold decrease in catalytic efficiency
S127A
-
active site mutant, orotate recognition mutant
T159V/V182A
3600fold decrease in catalytic efficiency
T159V/V182A/Y206F
20000fold decrease in catalytic efficiency
T159V/Y206F
780fold decrease in catalytic efficiency
V182A/Y206F
190fold decrease in catalytic efficiency
K93C
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K93C has no activity, affinities for the competitive inhibitor 6-azauridylate and UMP are significantly altered from the pattern with the wild type enzyme
C155S
D91A
D96A
K59A
K93A
K93C
Q215A
Q215A/R235A
Q215A/S154A
site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics
Q215A/Y217F
Q215A/Y217F/R235A
R235A
S154A
S154A/Q215A
Y217A
Y217F
Y217F/R235A
Q215A
R235A
S154A
Y217A
Saccharomyces cerevisiae ATCC 204508 / S288c
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site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics, the Y217A mutation results in large decreases in kcat/Km for ScOMPDC-catalyzed decarboxylation of both orotidine 5'-phosphate and 5-fluoroorotidine 5'-phosphate, because of the comparable effects of this mutation on rate-determining decarboxylation of enzyme-bound OMP and on the rate-determining enzyme conformational change for decarboxylation of 5-fluoroorotidine 5'-phosphate
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Y217F
Saccharomyces cerevisiae ATCC 204508 / S288c
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site-directed mutagenesis, the mutation results in an about 2.4fold decrease in kcat/Km for decarboxylation of 1-(beta-D-erythrofuranosyl)-orotic acid
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additional information
Q185A
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active site mutant, orotate recognition mutant
R160A/Y206F
340fold decrease in catalytic efficiency
C155S
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the mutant is more stable than the wild-type enzyme but retains the catalytic properties of the wild-type enzyme
D91A
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inactive mutant, reduced activity by 5 orders of magnitude, no substrate binding
D91A
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mutant with strongly reduced activity, incapable of binding substrate
D96A
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active site mutant with increased dissociation constants for various ligands and strongly reduced activity
D96A
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inactive mutant, reduced kcat-value by more than 5 orders of magnitude, 11fold decrease in the affinity for the substrate in the ground state
K59A
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active site mutant with increased dissociation constants for various ligands and strongly reduced activity
K93A
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inactive mutant, reduced activity by 5 orders of magnitude, no substrate binding
K93A
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mutant with strongly reduced activity, incapable of binding substrate
K93C
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inactive mutant, rescue of the mutant with bromethylamine restores activity
Q215A
mutant, effect of the mutation of the kinetic parameters for decarboxylation is determined
Q215A
site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics
Q215A
site-directed mutagenesis, the mutation results in an about 2.4fold decrease in kcat/Km for decarboxylation of 1-(beta-D-erythrofuranosyl)-orotic acid
Q215A/R235A
site-directed mutagenesis, mutation of residues in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics, the mutation causes a large decrease in the kinetic parameters for ScOMPDC-catalyzed decarboxylation of OMP, which are limited by the rate of the decarboxylation step, but much smaller decreases in the kinetic parameters for ScOMPDC-catalyzed decarboxylation of 5-fluoroorotidine 5'-phosphate, which are limited by the rate of enzyme conformational changes
Q215A/Y217F
site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics
Q215A/Y217F/R235A
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effect of the triple mutation on the catalytic activity toward OMP can be ascribed almost entirely to the loss of stabilizing interactions of the three excised side chains with the transition state for decarboxylation
Q215A/Y217F/R235A
site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics
Q215A/Y217F/R235A
site-directed mutagenesis, no dianion activation
Q215A/Y217F/R235A
site-directed mutagenesis, triple mutation results in only a 9fold decrease in kcat/Km for decarboxylation of 1-(beta-D-erythrofuranosyl)-orotic acid
R235A
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active site mutant with increased dissociation constants for various ligands
R235A
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mutation results in 12000fold decrease in catalytic efficiency with substrate orotidine 5'-phosphate and 75fold decrease with substrate 5-fluoroorotidine 5'-phosphate. The effect of the R235A mutation on the enzyme-catalyzed deuterium exchange is expressed predominantly as a change in the turnover number kex, whereas the effect on the enzyme-catalyzed decarboxylation of orotidine 5'-phosphate is expressed predominantly as a change in the Michaelis constant Km
R235A
site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics
R235A
site-directed mutagenesis, the mutation results in an about 2.4fold decrease in kcat/Km for decarboxylation of 1-(beta-D-erythrofuranosyl)-orotic acid
S154A
mutant, effect of the mutation of the kinetic parameters for decarboxylation is determined
S154A
site-directed mutagenesis, the stabilizing interactions between the 5-F and neighboring C-6 carbanion are strongly expressed at the rate-determining transition state for decarboxylation of FOMP catalyzed by S154A mutant ScOMPDC
S154A/Q215A
mutant, effect of the mutation of the kinetic parameters for decarboxylation is determined
Y217A
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active site mutant with increased dissociation constants for various ligands
Y217A
site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics, the Y217A mutation results in large decreases in kcat/Km for ScOMPDC-catalyzed decarboxylation of both orotidine 5'-phosphate and 5-fluoroorotidine 5'-phosphate, because of the comparable effects of this mutation on rate-determining decarboxylation of enzyme-bound OMP and on the rate-determining enzyme conformational change for decarboxylation of 5-fluoroorotidine 5'-phosphate
Y217F
site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics
Y217F
site-directed mutagenesis, the mutation results in an about 2.4fold decrease in kcat/Km for decarboxylation of 1-(beta-D-erythrofuranosyl)-orotic acid
Y217F/R235A
site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics
Q215A
Saccharomyces cerevisiae ATCC 204508 / S288c
-
site-directed mutagenesis, the mutation results in an about 2.4fold decrease in kcat/Km for decarboxylation of 1-(beta-D-erythrofuranosyl)-orotic acid
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Q215A
Saccharomyces cerevisiae ATCC 204508 / S288c
-
site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics
-
R235A
Saccharomyces cerevisiae ATCC 204508 / S288c
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site-directed mutagenesis, the mutation results in an about 2.4fold decrease in kcat/Km for decarboxylation of 1-(beta-D-erythrofuranosyl)-orotic acid
-
R235A
Saccharomyces cerevisiae ATCC 204508 / S288c
-
site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics
-
S154A
Saccharomyces cerevisiae ATCC 204508 / S288c
-
site-directed mutagenesis, the stabilizing interactions between the 5-F and neighboring C-6 carbanion are strongly expressed at the rate-determining transition state for decarboxylation of FOMP catalyzed by S154A mutant ScOMPDC
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additional information
Methanobacterium thermoautotrophicus
substitutions of hydrophobic residues in a pocket proximal to the carboxylate group of the substrate, i.e. Ile 96, Leu 123, and Val 155 with neutral hydrophilic residues decrease the value of kcat by as much as 400fold but have minimal effect on the value of kex for exchange of H6 of the 5-fluoro-UMP product analog with solvent deuterium
additional information
Methanobacterium thermoautotrophicus DSM 1053
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substitutions of hydrophobic residues in a pocket proximal to the carboxylate group of the substrate, i.e. Ile 96, Leu 123, and Val 155 with neutral hydrophilic residues decrease the value of kcat by as much as 400fold but have minimal effect on the value of kex for exchange of H6 of the 5-fluoro-UMP product analog with solvent deuterium
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additional information
the orotidine 5'-phosphate decarboxylase encoding gene, pm-ura3, from Pestalotiopsis microspora strain NK17 is utilized as a marker in the construction of a reusable system for gene scarless deletion, restoration, and tagging. As a positive marker, gene pm-ura3 can be used to targeted locus of interest in a start uracil auxotrophic host. It then can be replaced by any artificial DNA sequence, e.g. a mutated ORF, under the negative selection of 5-fluoroorotic acid. By this method, genes of interest can be edited in situ and the marker can be recycled. The system is applied to study the function of pm-mus53, it is observed that the gene has little effect on the nonhomologous end-joining process mediated by Agrobacterium tumefaciens-mediated transformation. The expression of a putative taxadiene synthase in taxol biosynthetic pathways of Pestalotiopsis microspora is investigated revealing that it is differentially expressed in solid and liquid medium. Method overview
additional information
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the orotidine 5'-phosphate decarboxylase encoding gene, pm-ura3, from Pestalotiopsis microspora strain NK17 is utilized as a marker in the construction of a reusable system for gene scarless deletion, restoration, and tagging. As a positive marker, gene pm-ura3 can be used to targeted locus of interest in a start uracil auxotrophic host. It then can be replaced by any artificial DNA sequence, e.g. a mutated ORF, under the negative selection of 5-fluoroorotic acid. By this method, genes of interest can be edited in situ and the marker can be recycled. The system is applied to study the function of pm-mus53, it is observed that the gene has little effect on the nonhomologous end-joining process mediated by Agrobacterium tumefaciens-mediated transformation. The expression of a putative taxadiene synthase in taxol biosynthetic pathways of Pestalotiopsis microspora is investigated revealing that it is differentially expressed in solid and liquid medium. Method overview
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additional information
construction of a chimeric fusion enzyme from the last two enzymes in the pyrimidine biosynthetic pathway in the inversed order by having a C-terminal orotate phosphoribosyltransferase (OPRT) and an N-terminal orotidine 5'-monophosphate decarboxylase (OMPDC) as OMPDC-OPRT in Plasmodium falciparum, the chimeric mutant acts as a bifunctional enzyme. The activitiy, although unstable, is stabilized by the substrate and product during purification and long-term storage. The kcat is selectively enhanced up to three orders of magnitude, while the Km is not much affected and remains at low micromolar levels when compared to the monofunctional enzymes. The fusion of the two enzymes creates a super-enzyme with perfect catalytic power and more flexibility
additional information
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construction of a chimeric fusion enzyme from the last two enzymes in the pyrimidine biosynthetic pathway in the inversed order by having a C-terminal orotate phosphoribosyltransferase (OPRT) and an N-terminal orotidine 5'-monophosphate decarboxylase (OMPDC) as OMPDC-OPRT in Plasmodium falciparum, the chimeric mutant acts as a bifunctional enzyme. The activitiy, although unstable, is stabilized by the substrate and product during purification and long-term storage. The kcat is selectively enhanced up to three orders of magnitude, while the Km is not much affected and remains at low micromolar levels when compared to the monofunctional enzymes. The fusion of the two enzymes creates a super-enzyme with perfect catalytic power and more flexibility
additional information
structure-function analysis of mutant enzymes, compared to the wild-type, overview
additional information
Saccharomyces cerevisiae ATCC 204508 / S288c
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structure-function analysis of mutant enzymes, compared to the wild-type, overview
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additional information
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construction of a null mutant, allelic replacement mutagenesis of pyrF, phenotype, overview, unlike the wild-type strain, an isogenic pyrF mutant is resistant to 5-fluoroorotic acid
