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Information on EC 4.1.1.23 - orotidine-5'-phosphate decarboxylase and Organism(s) Saccharomyces cerevisiae and UniProt Accession P03962
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4.1.1.23 orotidine-5'-phosphate decarboxylaseIUBMB Comments
The enzyme from higher eukaryotes is identical with EC 2.4.2.10 orotate phosphoribosyltransferase .
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Word Map
- 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
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
odcase, ump synthase, orotidine 5'-monophosphate decarboxylase, orotidine-5'-phosphate decarboxylase, omp decarboxylase, orotidine-5'-monophosphate decarboxylase, ompdc, orotidylate decarboxylase, orotidine monophosphate decarboxylase, orotidine 5'-phosphate decarboxylase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Orotidine 5'-monophosphate decarboxylase
-
Decarboxylase, orotidine 5'-phosphate
-
-
-
-
ODCase
OMP decarboxylase
OMP-DC
-
-
-
-
OMPDCase
-
-
-
-
OMPdecase
-
-
-
-
Orotate decarboxylase
-
-
-
-
Orotate monophosphate decarboxylase
-
-
-
-
Orotic decarboxylase
-
-
-
-
Orotidine 5'-monophosphate decarboxylase
Orotidine 5'-phosphate decarboxylase
-
-
-
-
Orotidine monophosphate decarboxylase
-
-
-
-
Orotidine phosphate decarboxylase
-
-
-
-
Orotidine-5'-monophosphate decarboxylase
Orotidylate decarboxylase
-
-
-
-
Orotidylic acid decarboxylase
-
-
-
-
Orotidylic decarboxylase
-
-
-
-
Orotodylate decarboxylase
-
-
-
-
UMP synthase
-
-
-
-
Uridine 5'-monophosphate synthase
-
-
-
-
ODCase
-
-
-
-
OMP decarboxylase
-
-
-
-
Orotidine 5'-monophosphate decarboxylase
-
-
-
-
Orotidine-5'-monophosphate decarboxylase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
orotidine 5'-phosphate = UMP + CO2
catalysis by OMPDC is due to stabilization of the decarboxylation transition state by interactions with the protein catalyst leading to a 1023-fold rate acceleration. The falloff in the second-order rate constants for OMPDC-catalyzed decarboxylation observed upon the truncation of the phosphodianion and the ribosyl phosphate from the substrate orotidine 5'-phosphate (OMP), catalytic mechanism, detailed overview. Interaction between the side chains of Ser154 and Gln215 wild-type ScOMPDC is required to hold the amide side chain in a position to interact with the substrate phosphodianion. The dianion binding interactions with Gln215, Tyr217, and Arg235 serve the exclusive function of activating OMPDC for catalysis at the pyrimidine binding site
orotidine 5'-phosphate = UMP + CO2
mechanism
-
orotidine 5'-phosphate = UMP + CO2
catalytic mechanism with freely reversible binding, a very limited contribution to the overall rate is made by chemical steps preceding decarboxylation
-
orotidine 5'-phosphate = UMP + CO2
direct decarboxylation mechanism, modeling with 6-carbanion derivatives of uracil analogues, overview
-
orotidine 5'-phosphate = UMP + CO2
reaction mechanism involving the active site aspartate residue Asp91, electrostatic stress furnishes the majority of the catalytic driving force for OMP decarboxylation, ylide generation is not the rate-limiting step in the ODCase reaction
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
decarboxylation
decarboxylation
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
orotidine-5'-phosphate carboxy-lyase (UMP-forming)
The enzyme from higher eukaryotes is identical with EC 2.4.2.10 orotate phosphoribosyltransferase .
CAS REGISTRY NUMBER
COMMENTARY
9024-62-8
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
1-(beta-D-erythrofuranosyl)-5-fluoroorotate
1-(beta-D-erythrofuranosyl)-5-fluorouracil + CO2
-
-
-
?
1-(beta-D-erythrofuranosyl)-orotate
1-(beta-D-erythrofuranosyl)uracil + CO2
-
-
-
?
2'-deoxyorotidine 5'-phosphate
2'-deoxyuridine 5'-phosphate + CO2
less effective than orotidine 5-phosphate
-
?
1-(beta-D-erythrofuranosyl)-5-fluoroorotic acid
1-(beta-D-erythrofuranosyl)-5-fluorouracil + CO2
-
truncated analog of the natural substrate orotidine 5'-monophosphate with enhanced reactivity towards decarboxylation. The vinyl carbanion-like transition state is stabilized by 3.5 kcal/mol by interactions with the 5-F substituent. Decarboxylation is activated by exogenous phosphite dianion, but the 5-F substituent results in only a 0.8 kcal stabilization of the transition state for the phosphite-activated reaction
-
-
?
1-(beta-D-erythrofuranosyl)orotic acid
1-(beta-D-erythrofuranosyl)uracil + CO2
-
truncated substrate
-
-
?
5'-deoxy-5-fluoroorotidine
? + CO2
-
truncated analog of the natural substrate orotidine 5'-monophosphate with enhanced reactivity towards decarboxylation. The 4'-CH3 and 4'-CH2OH groups of 5'-deoxy-5-fluoroorotidine and orotidine, respectively, result in identical destabilizations of the transition state for the unactivated decarboxylation of 2.9 kcal/mol. By contrast, the 4'-CH3 group of 5'-deoxy-5-fluoroorotidine and the 4'-CH2OH group of orotidine result in very different 4.7 and 8.3 kcal/mol destabilizations of the transition state for the phosphite-activated decarboxylation
-
-
?
Orotidine 5'-phosphate
?
-
final step in pyrimidine biosynthesis
-
-
?
Orotidine 5'-phosphate
UMP + CO2
-
-
-
?
Orotidine 5'-phosphate
UMP + CO2
enzyme/active site structure, mode of substrate binding
-
?
Orotidine 5'-phosphate
UMP + CO2
catalyzes the final step of pyrimidine biosynthesis
-
?
Orotidine 5'-phosphate
UMP + CO2
stepwise mechanism via a UMP carbanion intermediate, modeling of the transition state stabilization
-
-
?
2'-deoxyorotidine 5'-phosphate
2'-deoxyuridine 5'-phosphate + CO2
-
-
-
?
2'-deoxyorotidine 5'-phosphate
2'-deoxyuridine 5'-phosphate + CO2
-
-
-
-
?
4-Thioorotidine 5'-phosphate
4-Thiouridine 5'-phosphate + CO2
-
-
-
-
?
4-Thioorotidine 5'-phosphate
4-Thiouridine 5'-phosphate + CO2
-
nearly equally effective as orotidine 5'-phosphate
-
?
5-Fluoroorotidine 5'-phosphate
5-Fluorouridine 5'-phosphate + CO2
-
-
-
-
?
5-Fluoroorotidine 5'-phosphate
5-Fluorouridine 5'-phosphate + CO2
-
-
-
?
5-Fluoroorotidine 5'-phosphate
5-Fluorouridine 5'-phosphate + CO2
-
-
-
-
?
5-Fluoroorotidine 5'-phosphate
5-Fluorouridine 5'-phosphate + CO2
-
the 5-fluoro substituent results in a 3400fold increase in the first-order rate constant for deuterium exchange
-
-
?
Orotidine 5'-phosphate
UMP + CO2
-
-
-
-
?
Orotidine 5'-phosphate
UMP + CO2
-
catalytic mechanism involving protonation at O2 and a proposed Zn2+ interaction at O4, role of Lys-93 in catalysis
-
?
Orotidine 5'-phosphate
UMP + CO2
-
catalytic proficiency, activity does not depend on the formation of a covalent bond to the substrate, catalyzes the reaction through noncovalent binding interactions that involve only the functional groups of its constituent amino acids, catalytic mechanism, mechanism of transition state stabilization, active site structure, role of Lys-93
-
ir
Orotidine 5'-phosphate
UMP + CO2
-
enzyme has two functionally independent substrate binding sites
-
?
Orotidine 5'-phosphate
UMP + CO2
-
mechanism, carbanion intermediate is stabilized by simple electrostatic interaction with Lys-93, the driving force of reaction is ground state destabilization resulting from charge repulsion between the carboxyl of the substrate and Asp-91
-
?
Orotidine 5'-phosphate
UMP + CO2
-
the integrity of the network of the charged residues within the active site, Lys-59, Asp-91, Lys-93 and Asp-96, is essential for transition state stabilization, altered substrate is very tightly bound in the transition state, mechanism
-
?
Orotidine 5'-phosphate
UMP + CO2
-
catalyzes the critical final step in the pyrimidine biosynthetic pathway
-
?
Orotidine 5'-phosphate
UMP + CO2
-
catalyzes the final step of de novo pyrimidine nucleotide biosynthesis
-
?
Orotidine 5'-phosphate
UMP + CO2
-
production of UMP, the biosynthetic precursor of pyrimidine nucleotides
-
?
Orotidine 5'-phosphate
UMP + CO2
-
the enzyme is the most effective pure protein catalyst known in nature
-
-
?
Orotidine 5'-phosphate
UMP + CO2
-
act upon its substrate without the intervention of metals or other cofactors and without the formation of covalent bonds between the enzyme and the substrate, substrate binding forces the substrates scissile carboxylate group into the neighborhood of several charged groups at the active site, reaction mechanism, overview
-
-
?
Orotidine 5'-phosphate
UMP + CO2
-
the decarboxylase shows an extremely fast rate acceleration, 1017-fold rate enhancement, ODCase associates weakly with the substrate in the ground state, but then tightens its grip as the altered substrate approaches the chemical transition state, yielding a complex with an estimated dissociation constant Ktx of over 10-24 M
-
-
?
additional information
?
-
extraordinary specificity of OMPDC in binding the decarboxylation transition state with a higher affinity compared with the substrate orotidine 5'-phosphate. Substrate specificity and kinetic analysis, structure-function analysis, detailed overview
-
-
?
additional information
?
-
ScOMPDC also catalyzes decarboxylation of 1-(beta-D-erythrofuranosyl)-5-fluoroorotate (FEO), of 5-fluoroorotate (FO), and of 1-(beta-D-erythrofuranosyl)-orotic acid (EO). Open and the closed forms of enzyme ScOMPDC: phosphodianion gripper loop (with structural heterogeneity between organisms) and pyrimidine umbrella, structure, overview. Reaction mechanism and kinetics with different substrates, transition state analysis
-
-
?
additional information
?
-
two flexible loops close to form the active site cage: Pro202-Val220, on the left-hand side of each structure, interact with the substrate dianion, and Glu152-Thr165, on the right-hand side, interact with the pyrimidine ring. The tyrosyl phenol group stabilizes the closed form of ScOMPDC by hydrogen bonding to the substrate phosphodianion, and that the phenyl group of Y217 and F217 facilitates formation of the transition state for the rate-limiting conformational change
-
-
?
additional information
?
-
-
2-thioorotidine 5'-phosphate is 10000000fold less reactive than orotidine 5'-phosphate as substrate, not: 2-thiouridine 5'-phosphate
-
?
additional information
?
-
-
not: 2-thioorotidine 5-phosphate, undetectable activity with CMP-6-carboxylate and weak binding to ODCase
-
?
additional information
?
-
-
the yeast enzyme does not exhibit a measurable affinity for a substrate analogue in which the labile carboxylate group is replaced by a cationic substituent, the apo and ligand-bound forms of the enzyme show distinct open and closed forms, the closed form is catalytically competent
-
-
?
additional information
?
-
-
in reaction model phosphodianion binding interactions are utilized to stabilize a rare closed enzyme form that exhibits a high catalytic activity for decarboxylation. The thermodynamic barrier to formation of the productive catalytic complex from the inactive enzyme arises largely from the desolvation of the active site accompanying the conformational change and sequestration of the substrate from bulk solvent. The energetically unfavorable conformational change and desolvation of the active site are paid for by the binding energy available from the formation of strong phosphodianion-protein interactions in the desolvated environment present at the EC·S complex. The phosphodianion binding energy is recovered as transition state stabilization via the enhanced electrostatic and hydrogen bonding interactions at the transition state in the desolvated active site
-
-
?
additional information
?
-
-
the total transition-state stabilization for decarboxylation of orotidine 5'-phosphate via the UMP vinyl carbanion intermediate exceeds that for the formation of this carbanion by proton transfer from C-6 of UMP to the enzyme by ca.17 kcal/mol. A large portion of the total transition-state stabilization for the decarboxylation of orotidine 5'-monophosphate can be accounted for by stabilization of the enzyme-bound vinyl carbanion intermediate of the stepwise reaction
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
Orotidine 5'-phosphate
?
-
final step in pyrimidine biosynthesis
-
-
?
Orotidine 5'-phosphate
UMP + CO2
-
-
-
?
Orotidine 5'-phosphate
UMP + CO2
catalyzes the final step of pyrimidine biosynthesis
-
?
Orotidine 5'-phosphate
UMP + CO2
-
-
-
-
?
Orotidine 5'-phosphate
UMP + CO2
-
catalyzes the critical final step in the pyrimidine biosynthetic pathway
-
?
Orotidine 5'-phosphate
UMP + CO2
-
catalyzes the final step of de novo pyrimidine nucleotide biosynthesis
-
?
Orotidine 5'-phosphate
UMP + CO2
-
production of UMP, the biosynthetic precursor of pyrimidine nucleotides
-
?
Orotidine 5'-phosphate
UMP + CO2
-
the enzyme is the most effective pure protein catalyst known in nature
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Zinc
Zn2+
additional information
Zinc
-
zinc, rather than a proton may be largely responsible for neutralizing charge development in the transition state for OMP decarboxylation
Zn2+
-
mechanism may include participation of Zn2+, which interacts at O4 with the substrate
Zn2+
-
native ODCase expressed in yeast contains zinc, but not recombinant ODCase expressed in Escherichia coli, zinc is not involved in substrate decarboxylation
additional information
-
no metal cofactor, e.g. Zn2+ or other transition metal ions
additional information
-
zinc-free fully active recombinant ODCase expressed in Escherichia coli, metals do not directly participate in the decarboxylation mechanism
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2'-deoxyuridine 5'-phosphate
competitive inhibition, at higher concentrations
6-hydroxyuridine 5'-monophosphate
strong binding of 6-hydroxyuridine 5'-monophosphate (BMP) to OMPDC induces a protein conformational change. This includes closure of the phosphodianion gripper loop (Pro202-Val220) and pyrimidine umbrella (Glu152-Thr165) over the inhibitor, which locks BMP in a protein cage. Interactions of the ligand phosphodianion with the amide side chain of Gln215, the phenol side chain of Tyr217, the guanidine side chain of Arg235, which sits on the protein surface adjacent to the gripper loop and functions cooperatively with the loop side chains in activating OMPDC for catalysis, and with backbone amides from Gly234 and Arg235
4-thiouridine 5'-phosphate
-
competitive inhibition, stronger inhibitor than UMP
5,6-dihydro-6-sulfonyl-OMP
-
inhibitor with high affinity for the enzyme
5,6-dihydro-6-sulfonyl-UMP
-
inhibitor with high affinity for the enzyme
5-(2-(N-(2-Acetamidoethyl)carbamyl)ethyl)-6-azauridine 5'phosphate
-
maximal inhibition at pH 8.3
6-hydroxy UMP
-
inhibits activity with orotidine and orotidine 5'-phosphate, mutant enzyme C155S
6-hydroxyUMP
-
a transition state analogue inhibitor, binding structure in complex with the enzyme, overview
oxipurinol nucleotides
-
potent, competitive, bimodal. The inhibition of the enzyme by oxipurinol nucleotides is primarily responsible for the increased urinary excretion of orotic acid and orotidine in patients treated with allopurinol
1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid
-
high affinity inhibitor
1-Ribosyloxipurinol 5'-phosphate
-
most effective oxipurinol nucleotide inhibitor
6-thiocarboxamidouridine 5'-phosphate
-
competitive, very strong, reversible inhibition
additional information
-
not inhibited by 2-thioorotidine 5'-phosphate
-
additional information
-
not inhibited by 6-carboxamidouridine 5-phosphate, recombinant ODCase expressed in Escherichia coli is not inhibited by 1,3-dimercaptopropanol and EDTA
-
additional information
-
not inhibited by zinc-chelating agents, e.g. EDTA
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
D-erythritol 4-phosphate
activates the decarboxylation of 5-fluoroorotate. This activation is due to the utilization of binding energy from interactions between OMPDC and activator
D-glycerol 3-phosphate
activates the decarboxylation of 5-fluoroorotate.
HPO32-
-
decarboxylation of substrate analog 5'-deoxy-5-fluoroorotidine is activated. Decarboxylation of truncated substrate analog 1-(beta-D-erythrofuranosyl)-5-fluoroorotic acid is activated by exogenous phosphite dianion, but the 5-F substituent results in only a 0.8 kcal stabilization of the transition state for the phosphite-activated reaction
additional information
enzyme ScOMPDC-catalyzed decarboxylation of 5-fluoroorotate is stabilized by 5.2, 7.2, and 9.0 kcal/mol, respectively, by 1.0 M phosphite dianion, D-glycerol 3-phosphate and D-erythritol 4-phosphate, so that binding interactions between both the substrate phosphodianion and the ribosyl hydroxyls are utilized to activate ScOMPDC for catalysis
-
phosphite dianion
strong phosphite dianion activation of ScOMPDC-catalyzed decarboxylation of of 1-(beta-D-erythrofuranosyl)-5-fluoroorotate (FEO), of 5-fluoroorotate (FO) and of 1-(beta-D-erythrofuranosyl)-orotic acid. Utilization of intrinsic dianion energy
phosphite dianion
the activation with substrate 1-(beta-D-erythrofuranosyl)-orotate is due to the utilization of binding energy from interactions between OMPDC and activator to drive a complex conformational change from inactive open OMPDC (EO) to the active closed caged complex (EC), where EC is stabilized relative to EO by interactions between dianions and the side chains of Q215, Y217, and R235
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0052
2'-deoxyorotidine 5'-phosphate
pH 7.2, 25°C, T100A mutant
0.0054
2'-deoxyorotidine 5'-phosphate
pH 7.2, 25°C, wild-type enzyme
0.01
2'-deoxyorotidine 5'-phosphate
pH 7.2, 25°C, D37A mutant
0.008
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, wild-type enzyme
0.055
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant S154A
0.086
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant S154A/Q215A
0.096
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A
0.42
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Y217F
0.58
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant R235A
0.62
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Y217A
0.65
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/R235A
0.92
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/Y271F
0.29 - 1.4
orotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/Y271F
0.35 - 1.4
orotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/R235A
2.2 - 12.9
orotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/Y217F/R235A
6.1 - 27.1
orotidine 5'-phosphate
pH 7.1, 25°C, mutant Y217F/R235A
0.0006
orotidine 5'-phosphate
-
22-25°C, pH 7.2, recombinant ODCase expressed in Escherichia coli
0.0007
orotidine 5'-phosphate
-
22°C, native ODCase expressed in yeast
0.001 - 0.002
orotidine 5'-phosphate
-
Km value is very dependent on the NaCl concentration, NaCl increases the Km value
30
orotidine 5'-phosphate
-
value is higher than 30 mM, pH 7.2, 23°C, mutant enzyme C155S
additional information
additional information
kinetic analysis
-
additional information
additional information
kinetic analysis of wild-type and mutant enzymes with substrate orotidine 5'-phosphate
-
additional information
additional information
kinetic analysis of wild-type and mutant enzymes with substrates orotidine 5'-phosphate and 5-fluoroorotidine 5'-phosphate, rate and equilibrium constants for the conformational change that traps 5-fluoroorotidine 5'-phosphate at the enzyme active site
-
additional information
additional information
substrate specificity and kinetic analysis, overview
-
additional information
additional information
-
kinetic data and mechanism
-
additional information
additional information
-
kinetic properties, catalytic proficiency/efficiency
-
additional information
additional information
-
kinetics and thermodynamics
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0017
2'-deoxyorotidine 5'-phosphate
pH 7.2, 25°C, D37A mutant
0.15
2'-deoxyorotidine 5'-phosphate
pH 7.2, 25°C, wild-type enzyme
0.16
2'-deoxyorotidine 5'-phosphate
pH 7.2, 25°C, T100A mutant
4.7
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/R235A
6.6
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant S154A/Q215A
8.2
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Y217A
49
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/Y271F
95
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, wild-type enzyme
190
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A
430
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Y217F
0.00048
orotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/Y217F/R235A
0.19 - 0.2
orotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/R235A
92
5-Fluoroorotidine 5'-phosphate
-
mutant R235A, pH 7.1, 25°C, presence of 0.1 M NaCl
95
5-Fluoroorotidine 5'-phosphate
-
wild-type, pH 7.1, 25°C, presence of 0.1 M NaCl
1
orotidine 5'-phosphate
-
mutant R235A, pH 7.1, 25°C, presence of 0.1 M NCl
14 - 20
orotidine 5'-phosphate
-
pH 7.2, 25°C, not affected by NaCl concentration
15
orotidine 5'-phosphate
-
wild-type, pH 7.1, 25°C, presence of 0.1 M NaCl
19
orotidine 5'-phosphate
-
22-25°C, pH 7.2, recombinant ODCase expressed in Escherichia coli
additional information
additional information
-
high catalytic proficiency
-
additional information
additional information
-
very high catalytic proficiency
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00002
1-(beta-D-erythrofuranosyl)-orotate
pH 7.0, 25°C, wild-type enzyme
0.028
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/Y217F/R235A
0.82
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Y217F/R235A
7.23
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/R235A
13.2
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Y217A
53.3
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/Y271F
76.7
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant S154A/Q215A
158.6
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant R235A
290.9
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant S154A
1023.9
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Y217F
1979
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A
11875
5-Fluoroorotidine 5'-phosphate
pH 7.1, 25°C, wild-type enzyme
0.000037 - 0.00022
orotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/Y217F/R235A
0.0041 - 0.018
orotidine 5'-phosphate
pH 7.1, 25°C, mutant Y217F/R235A
0.014 - 0.054
orotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/R235A
3.4 - 17
orotidine 5'-phosphate
pH 7.1, 25°C, mutant Q215A/Y271F
3
1-(beta-D-erythrofuranosyl)orotic acid
-
mutant Q215A/Y217F/R235A, pH 7.1, 25°C
4.2
1-(beta-D-erythrofuranosyl)orotic acid
-
mutant Q215A/R235A, pH 7.1, 25°C
4.6
1-(beta-D-erythrofuranosyl)orotic acid
-
mutant Q215A/Y217F, pH 7.1, 25°C
10
1-(beta-D-erythrofuranosyl)orotic acid
-
mutant Y217F/R235A, pH 7.1, 25°C
11
1-(beta-D-erythrofuranosyl)orotic acid
-
mutant Q215A, pH 7.1, 25°C
12
1-(beta-D-erythrofuranosyl)orotic acid
-
mutant Y217F, pH 7.1, 25°C
26
1-(beta-D-erythrofuranosyl)orotic acid
-
mutant R235A, pH 7.1, 25°C
0.00004
orotidine 5'-phosphate
-
mutant Q215A/Y217F/R235A, pH 7.1, 25°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0000035
6-thiocarboxamidouridine 5'-phosphate
-
recombinant ODCase expressed in Escherichia coli
0.000000009
barbiturate ribonucleoside 5'-monophosphate
-
in 50 mM Tris (pH 7.5), 20 mM dithiothreitol, and 40 mM NaCl, at 22°C
0.000005
pyrazofurin-5'-monophosphate
-
in 50 mM Tris (pH 7.5), 20 mM dithiothreitol, and 40 mM NaCl, at 22°C
0.000064
6-azauridine 5'-phosphate
pH 7.4, 25°C, wild-type enzyme
0.00041
xanthosine 5'-phosphate
pH 7.4, 25°C, wild-type enzyme
additional information
additional information
-
inhibition kinetics
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
39.3
-
22-25°C, pH 7.2, recombinant ODCase expressed in Escherichia coli
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.1
6.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
substrate specificity and kinetic analysis, structure-function analysis, detailed overview
additional information
the phosphodianion gripper loop [Pro202-Val220] is important for catalysis
additional information
the role of flexible loops in enzyme catalysis, important interactions of Gln215, Tyr217, and Arg235 side chains from the phosphodianion gripper loop with the ligand phosphodianion, structure-function analysis, overview. Mechanism by which ionic and hydrogen-bonding interactions of side chains from the gripper loop, and Arg235, with the phosphodianion of OMP, or with HPi, are utilized in stabilization of the transition state for OMPDC-catalyzed decarboxylation of OMP, deprotonation of UMP, and the corresponding reactions of the phosphodianion truncated substrates 1-(beta-D-erythrofuranosyl)orotic acid and FEU, respectively, at a site 10 A distant from the gripper loop
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
27000
-
x * 27000, about, recombinant ODCase expressed in Escherichia coli, SDS-PAGE
29500
-
sucrose density gradient centrifugation, at low protein concentration, in absence of ligands that bind at the catalytic site. The enzyme exists as dimer at high protein concentrations
64000
-
sucrose density gradient centrifugation, at high protein concentration, in presence of 0.05 mM 6-azauridine 5'-phosphate or 0.002 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid. The enzyme exists as monomer at low protein concentrations
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
-
x * 27000, about, recombinant ODCase expressed in Escherichia coli, SDS-PAGE
dimer
homodimer
-
active form, two independently operating active sites per dimer, located at the interface between subunits
additional information
-
QM/MM enzyme simulations, free enzyme and enzyme bound to 6-hydroxy-UMP, QM/MM and metadynamics, enzyme structure analysis, overview
dimer
-
catalytically active form, substrate-induced enzyme dimerization
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
no posttranslational modifications in recombinant ODCase expressed in Escherichia coli, but presumably in native ODCase from yeast, in which the N-terminus is blocked
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 100 mM Tris-HCl, pH 8.4, 2.12 M ammonium sulfate (enzyme in complex with 4 and 10) or using 100 mM Tris-HCl, pH 8.4, 1.4 M ammonium sulfate (enzyme in complex with pyrazofurin-5'-monophosphate)
-
in complex with different ligands, e.g. 6-hydroxyuridine 5'-phosphate
-
molecular dynamics simulations on X-ray structure of the enzyme in its free form as well as in complex with ligands 1-(5'-phospho-D-ribofuranosyl) barbituric acid, orotidine 5'-monophosphate, and 6-phosphonouridine 5'-monophosphate
-
orotidine 5'-monophosphate decarboxylase complexed with 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid
-
PDB ID 1DQX, free enzyme and enzyme bound to 6-hydroxy-UMP, crystal structure analysis of the enzyme in presence or absence of a potenial transition state analogue, comparison to predicted structure by QM/MM enzyme simulations, overview
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics
Q215A/Y217F/R235A
R235A
S154A
S154A/Q215A
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
Y217F/R235A
C155S
D91A
D96A
K59A
K93A
K93C
Q215A
Q215A/Y217F/R235A
-
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
R235A
Y217A
-
active site mutant with increased dissociation constants for various ligands
additional information
structure-function analysis of mutant enzymes, compared to the wild-type, overview
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/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
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
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
C155S
-
the mutant is more stable than the wild-type enzyme but retains the catalytic properties of the wild-type enzyme
D91A
-
inactive mutant, reduced activity by 5 orders of magnitude, no substrate binding
D91A
-
mutant with strongly reduced activity, incapable of binding substrate
D96A
-
active site mutant with increased dissociation constants for various ligands and strongly reduced activity
D96A
-
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
-
active site mutant with increased dissociation constants for various ligands and strongly reduced activity
K93A
-
inactive mutant, reduced activity by 5 orders of magnitude, no substrate binding
K93A
-
mutant with strongly reduced activity, incapable of binding substrate
K93C
-
inactive mutant, rescue of the mutant with bromethylamine restores activity
R235A
-
active site mutant with increased dissociation constants for various ligands
R235A
-
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
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
-
half-life: 10 min. Nucleotide inhibitors stabilize against inactivation at 37°C
additional information
-
the recombinant zinc-free ODCase expressed in Escherichia coli is more thermolabile than the zinc-containing ODCase expressed in yeast
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
1-ribosyloxipurinol 5'-phosphate prevents loss of activity during preincubation in absence of substrate, when the inhibitor concentration is high enough to inhibit the enzyme substantially
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 20% glycerol, retention of full activity for more than 2 years
-
0-4°C, stable in 10 mM potassium phosphate buffer, pH 5.8-7.5, containing 5 mM 2-mercaptoethanol for several weeks
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli by nickel affinity chromatography, tag cleavage with thrombin, and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli
recombinant expression of His6 or His10-tagged wild-type and mutant enzymes in Escherichia coli
ura3 gene, wild-type and mutant ODCase, expression in Escherichia coli SS6130
expression of mutant enzymes C155S and D96A/C155S in Escherichia coli
-
ura3 gene expression in Escherichia coli SS6130, expression in yeast
-
wild-type and mutant ODCase, expression in Escherichia coli SS6130
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Fyfe, J.A.; Miller, R.L.; Krenitsky, T.A.
Kinetic properties and inhibition of orotidine 5'-phosphate decarboxylase. Effects of some allopurinol metabolites on the enzyme
J. Biol. Chem.
248
3801-3809
1973
Saccharomyces cerevisiae
Yoshimoto, A.; Umezu, K.; Kobayashi, K.; Tomita, K.
Orotidylate decarboxylase (yeast)
Methods Enzymol.
51
74-79
1978
Saccharomyces cerevisiae
Brody, R.S.; Westheimer, F.H.
The purification of orotidine-5'-phosphate decarboxylase from yeast by affinity chromatography
J. Biol. Chem.
254
4238-4244
1979
Saccharomyces cerevisiae
Reiter, S.; Grbner, W.
Orotidine-5'-phosphate decarboxylase
Methods Enzym. Anal. , 3rd Ed. (Bergmeyer, H. U. , ed. )
4
338-346
1984
Saccharomyces cerevisiae, Mus musculus, Rattus norvegicus
-
Levine, H.L.; Brody, R.S.; Westheimer, F.H.
Inhibition of orotidine-5'-phosphate decarboxylase by 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid, 6-azauridine 5'-phosphate and uridine 5'-phosphate
Biochemistry
19
4993-3999
1980
Saccharomyces cerevisiae
Smiley, J.A.; Paneth, P.; O'Leary, M.H.; Bell, J.B.; Jones, M.E.
Investigation of the enzymatic mechanism of yeast orotidine-5'-monophosphate decarboxylase using 13C kinetic isotope effects
Biochemistry
25
6216-6223
1991
Saccharomyces cerevisiae
Acheson, S.A.; Bell, J.B.; Jones, M.E.; Wolfenden, R.
Orotidine-5'-monophosphate decarboxylase catalysis: kinetic isotope effects and the state of hybridization of a bound transition-state analogue
Biochemistry
29
3198-3202
1990
Saccharomyces cerevisiae, Saccharomyces cerevisiae 15C
Miller, B.G.; Traut, T.W.; Wolfenden, R.
A role for zinc in OMP decarboxylase, an unusually proficient enzyme
J. Am. Chem. Soc.
120
2666-2667
1998
Saccharomyces cerevisiae
-
Shostak, K.; Jones, E.
Orotidylate decarboxylase: insights into the catalytic mechanism from substrate specificity studies
Biochemistry
31
12155-12161
1992
Saccharomyces cerevisiae
Jones, M.E.
Orotidylate decarboxylase of yeast and man
Curr. Top. Cell. Regul.
33
331-342
1992
Saccharomyces cerevisiae, Homo sapiens, Mus musculus
Bell, J.B.; Jones, M.E.
Purification and characterization of yeast orotidine 5'-monophosphate decarboxylase overexpressed from plasmid PGU2
J. Biol. Chem.
266
12662-12667
1991
Saccharomyces cerevisiae, Saccharomyces cerevisiae 15C
Bell, J.B.; Jones, M.E.; Carter, C.W.
Crystallization and yeast orotidine 5'-monophosphate decarboxylase complexed with 1-(5'-phospho-beta-D-ribofuranosyl) barbituric acid
Proteins Struct. Funct. Genet.
9
143-151
1991
Saccharomyces cerevisiae
Miller, B.G.; Wolfenden, R.
Catalytic proficiency: the unusual case of OMP decarboxylase
Annu. Rev. Biochem.
71
847-885
2002
Bacillus subtilis, Saccharomyces cerevisiae, Escherichia coli
Smiley, J.A.; DelFraino, B.J.; Simpson, B.A.
Hydrogen isotope tracing in the reaction of orotidine-5'-monophosphate decarboxylase
Arch. Biochem. Biophys.
412
267-271
2003
Saccharomyces cerevisiae
Cui, W.; DeWitt, J.G.; Miller, S.M.; Wu, W.
No metal cofactor in orotidine 5'-monophosphate decarboxylase
Biochem. Biophys. Res. Commun.
259
133-135
1999
Saccharomyces cerevisiae, Saccharomyces cerevisiae BJ5464
Porter, D.J.T.; Short, S.A.
Yeast orotidine-5'-phosphate decarboxylase: steady-state and pre-steady-state analysis of the kinetic mechanism of substrate decarboxylation
Biochemistry
39
11788-11800
2000
Saccharomyces cerevisiae
Rishavy, M.A.; Cleland, W.W.
Determination of the mechanism of orotidine 5'-monophosphate decarboxylase by isotope effects
Biochemistry
39
4569-4574
2000
Saccharomyces cerevisiae
Miller, B.G.; Butterfoss, G.L.; Short, S.A.; Wolfenden, R.
Role of enzyme-ribofuranosyl contacts in the ground state and transition state for orotidine 5'-phosphate decarboxylase: a role for substrate destabilization?
Biochemistry
40
6227-6232
2001
Saccharomyces cerevisiae (P03962), Saccharomyces cerevisiae
Smiley, J.A.; Saleh, L.
Active site probes for yeast OMP decarboxylase: inhibition constants of UMP and thio-substituted UMP analogues and greatly reduced activity toward CMP-6-carboxylate
Bioorg. Chem.
27
297-306
1999
Saccharomyces cerevisiae, Saccharomyces cerevisiae BJ5424
-
Miller, B.G.; Smiley, J.A.; Short, S.A.; Wolfenden, R.
Activity of yeast orotidine-5'-phosphate decarboxylase in the absence of metals
J. Biol. Chem.
274
23841-23843
1999
Saccharomyces cerevisiae, Saccharomyces cerevisiae BJ5424
Miller, B.G.; Snider, M.J.; Wolfenden, R.; Short, S.A.
Dissecting a charged network at the active site of orotidine-5'-phosphate decarboxylase
J. Biol. Chem.
276
15174-15176
2001
Saccharomyces cerevisiae
Sievers, A.; Wolfenden, R.
The effective molarity of the substrate phosphoryl group in the transition state for yeast OMP decarboxylase
Bioorg. Chem.
33
45-52
2005
Saccharomyces cerevisiae
Callahan, B.P.; Bell, A.F.; Tonge, P.J.; Wolfenden, R.
A Raman-active competitive inhibitor of OMP decarboxylase
Bioorg. Chem.
34
59-65
2006
Saccharomyces cerevisiae
Amyes, T.L.; Richard, J.P.; Tait, J.J.
Activation of orotidine 5'-monophosphate decarboxylase by phosphite dianion: the whole substrate is the sum of two parts
J. Am. Chem. Soc.
127
15708-15709
2005
Saccharomyces cerevisiae
Lewis, C.A.; Wolfenden, R.
Indiscriminate binding by orotidine 5-phosphate decarboxylase of uridine 5-phosphate derivatives with bulky anionic c6 substituents
Biochemistry
46
13331-13343
2007
Saccharomyces cerevisiae
Callahan, B.P.; Miller, B.G.
OMP decarboxylase - An enigma persists
Bioorg. Chem.
35
465-469
2007
Saccharomyces cerevisiae
Wong, F.M.; Capule, C.C.; Wu, W.
Stability of the 6-carbanion of uracil analogues: mechanistic implications for model reactions of orotidine-5-monophosphate decarboxylase
Org. Lett.
8
6019-6022
2006
Saccharomyces cerevisiae
Barnett, S.A.; Amyes, T.L.; Wood, B.M.; Gerlt, J.A.; Richard, J.P.
Dissecting the total transition state stabilization provided by amino acid side chains at orotidine 5-monophosphate decarboxylase: a two-part substrate approach
Biochemistry
47
7785-7787
2008
Saccharomyces cerevisiae (P03962), Saccharomyces cerevisiae
Van Vleet, J.L.; Reinhardt, L.A.; Miller, B.G.; Sievers, A.; Wallace Cleland, W.
Carbon isotope effect study on orotidine 5-monophosphate decarboxylase: Support for an anionic intermediate
Biochemistry
47
798-803
2008
Saccharomyces cerevisiae
Amyes, T.L.; Wood, B.M.; Chan, K.; Gerlt, J.A.; Richard, J.P.
Formation and stability of a vinyl carbanion at the active site of orotidine 5-monophosphate decarboxylase: pKa of the C-6 proton of enzyme-bound UMP
J. Am. Chem. Soc.
130
1574-1575
2008
Saccharomyces cerevisiae
Meza-Avina, M.E.; Wei, L.; Buhendwa, M.G.; Poduch, E.; Bello, A.M.; Pai, E.F.; Kotra, L.P.
Inhibition of orotidine 5-monophosphate decarboxylase and its therapeutic potential
Mini Rev. Med. Chem.
8
239-247
2008
Bacillus subtilis, Saccharomyces cerevisiae, Escherichia coli, Homo sapiens, Plasmodium falciparum, Plasmodium vivax, Methanococcus thermoautotrophicum
Meza-Avina, M.E.; Wei, L.; Liu, Y.; Poduch, E.; Bello, A.M.; Mishra, R.K.; Pai, E.F.; Kotra, L.P.
Structural determinants for the inhibitory ligands of orotidine-5'-monophosphate decarboxylase
Bioorg. Med. Chem.
18
4032-4041
2010
Saccharomyces cerevisiae, Helicobacter pylori, Homo sapiens, Methanothermobacter thermautotrophicus, Staphylococcus aureus, Plasmodium falciparum
Amyes, T.L.; Ming, S.A.; Goldman, L.M.; Wood, B.M.; Desai, B.J.; Gerlt, J.A.; Richard, J.P.
Orotidine 5-monophosphate decarboxylase: transition state stabilization from remote protein-phosphodianion interactions
Biochemistry
51
4630-4632
2012
Saccharomyces cerevisiae
Goryanova, B.; Spong, K.; Amyes, T.L.; Richard, J.P.
Catalysis by orotidine 5-monophosphate decarboxylase: effect of 5-fluoro and 4-substituents on the decarboxylation of two-part substrates
Biochemistry
52
537-546
2013
Saccharomyces cerevisiae
Goryanova, B.; Goldman, L.M.; Amyes, T.L.; Gerlt, J.A.; Richard, J.P.
Role of a guanidinium cation-phosphodianion pair in stabilizing the vinyl carbanion intermediate of orotidine 5-phosphate decarboxylase-catalyzed reactions
Biochemistry
52
7500-7511
2013
Saccharomyces cerevisiae
Tsang, W.Y.; Wood, B.M.; Wong, F.M.; Wu, W.; Gerlt, J.A.; Amyes, T.L.; Richard, J.P.
Proton transfer from C-6 of uridine 5-monophosphate catalyzed by orotidine 5-monophosphate decarboxylase: formation and stability of a vinyl carbanion intermediate and the effect of a 5-fluoro substituent
J. Am. Chem. Soc.
134
14580-14594
2012
Saccharomyces cerevisiae
Jamshidi, S.; Jalili, S.; Rafii-Tabar, H.
Study of orotidine 5-monophosphate decarboxylase in complex with the top three OMP, BMP, and PMP ligands by molecular dynamics simulation
J. Biomol. Struct. Dyn.
33
404-417
2015
Saccharomyces cerevisiae
Richard, J.P.; Amyes, T.L.; Reyes, A.C.
Orotidine 5'-monophosphate decarboxylase probing the limits of the possible for enzyme catalysis
Acc. Chem. Res.
51
960-969
2018
Saccharomyces cerevisiae (P03962), Saccharomyces cerevisiae ATCC 204508 / S288c (P03962)
Goryanova, B.; Goldman, L.M.; Ming, S.; Amyes, T.L.; Gerlt, J.A.; Richard, J.P.
Rate and equilibrium constants for an enzyme conformational change during catalysis by orotidine 5'-monophosphate decarboxylase
Biochemistry
54
4555-4564
2015
Saccharomyces cerevisiae (P03962), Saccharomyces cerevisiae ATCC 204508 / S288c (P03962)
Goldman, L.M.; Amyes, T.L.; Goryanova, B.; Gerlt, J.A.; Richard, J.P.
Enzyme architecture deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5'-monophosphate decarboxylase
J. Am. Chem. Soc.
136
10156-10165
2014
Saccharomyces cerevisiae (P03962), Saccharomyces cerevisiae ATCC 204508 / S288c (P03962)
Reyes, A.C.; Amyes, T.L.; Richard, J.P.
Enzyme architecture Erection of active orotidine 5'-monophosphate decarboxylase by substrate-induced conformational changes
J. Am. Chem. Soc.
139
16048-16051
2017
Saccharomyces cerevisiae (P03962), Saccharomyces cerevisiae ATCC 204508 / S288c (P03962)
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