Literature summary for 4.1.1.23 extracted from

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 (2015), Biochemistry, 54, 4555-4564 .

Search for more literature for 4.1.1.23

Cloned(Commentary)

Cloned (Comment)	Organism
recombinant expression of His6 or His10-tagged wild-type and mutant enzymes in Escherichia coli	Saccharomyces cerevisiae

Protein Variants

Protein Variants	Comment	Organism
additional information	structure-function analysis of mutant enzymes, compared to the wild-type, overview	Saccharomyces cerevisiae
Q215A	site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics	Saccharomyces cerevisiae
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	Saccharomyces cerevisiae
Q215A/S154A	site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics	Saccharomyces cerevisiae
Q215A/Y217F	site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics	Saccharomyces cerevisiae
Q215A/Y217F/R235A	site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics	Saccharomyces cerevisiae
R235A	site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics	Saccharomyces cerevisiae
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	Saccharomyces cerevisiae
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	Saccharomyces cerevisiae
Y217F	site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics	Saccharomyces cerevisiae
Y217F/R235A	site-directed mutagenesis, mutation of a residue in the phosphodianion gripper loop reducing the catalytic efficiency and altering kinetics	Saccharomyces cerevisiae

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
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	Saccharomyces cerevisiae
0.008	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, wild-type enzyme	Saccharomyces cerevisiae
0.055	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant S154A	Saccharomyces cerevisiae
0.086	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant S154A/Q215A	Saccharomyces cerevisiae
0.096	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Q215A	Saccharomyces cerevisiae
0.42	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Y217F	Saccharomyces cerevisiae
0.58	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant R235A	Saccharomyces cerevisiae
0.62	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Y217A	Saccharomyces cerevisiae
0.65	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Q215A/R235A	Saccharomyces cerevisiae
0.92	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Q215A/Y271F	Saccharomyces cerevisiae

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
Orotidine 5'-phosphate	Saccharomyces cerevisiae	-	UMP + CO2	-	?
Orotidine 5'-phosphate	Saccharomyces cerevisiae ATCC 204508 / S288c	-	UMP + CO2	-	?

Organism

Organism	UniProt	Comment	Textmining
Saccharomyces cerevisiae	P03962	-	-
Saccharomyces cerevisiae ATCC 204508 / S288c	P03962	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli by nickel affinity chromatography, tag cleavage with thrombin, and gel filtration	Saccharomyces cerevisiae

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
1-(beta-D-erythrofuranosyl)-orotate	-	Saccharomyces cerevisiae	1-(beta-D-erythrofuranosyl)uracil + CO2	-	?
1-(beta-D-erythrofuranosyl)-orotate	-	Saccharomyces cerevisiae ATCC 204508 / S288c	1-(beta-D-erythrofuranosyl)uracil + CO2	-	?
5-fluoroorotidine 5'-phosphate	-	Saccharomyces cerevisiae	5-fluoro-UMP + CO2	-	?
5-fluoroorotidine 5'-phosphate	-	Saccharomyces cerevisiae ATCC 204508 / S288c	5-fluoro-UMP + CO2	-	?
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	Saccharomyces cerevisiae	?	-	?
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	Saccharomyces cerevisiae ATCC 204508 / S288c	?	-	?
Orotidine 5'-phosphate	-	Saccharomyces cerevisiae	UMP + CO2	-	?
Orotidine 5'-phosphate	-	Saccharomyces cerevisiae ATCC 204508 / S288c	UMP + CO2	-	?

Synonyms

Synonyms	Comment	Organism
OMPDC	-	Saccharomyces cerevisiae
Orotidine 5'-monophosphate decarboxylase	-	Saccharomyces cerevisiae
ScOMPDC	-	Saccharomyces cerevisiae

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
25	-	assay at	Saccharomyces cerevisiae

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
4.7	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Q215A/R235A	Saccharomyces cerevisiae
6.6	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant S154A/Q215A	Saccharomyces cerevisiae
8.2	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Y217A	Saccharomyces cerevisiae
16	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant S154A	Saccharomyces cerevisiae
49	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Q215A/Y271F	Saccharomyces cerevisiae
92	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant R235A	Saccharomyces cerevisiae
95	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, wild-type enzyme	Saccharomyces cerevisiae
190	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Q215A	Saccharomyces cerevisiae
430	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Y217F	Saccharomyces cerevisiae

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.1	-	assay at	Saccharomyces cerevisiae

General Information

General Information	Comment	Organism
additional information	the phosphodianion gripper loop [Pro202-Val220] is important for catalysis	Saccharomyces cerevisiae

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
0.028	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Q215A/Y217F/R235A	Saccharomyces cerevisiae
0.82	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Y217F/R235A	Saccharomyces cerevisiae
7.23	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Q215A/R235A	Saccharomyces cerevisiae
13.2	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Y217A	Saccharomyces cerevisiae
53.3	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Q215A/Y271F	Saccharomyces cerevisiae
76.7	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant S154A/Q215A	Saccharomyces cerevisiae
158.6	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant R235A	Saccharomyces cerevisiae
290.9	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant S154A	Saccharomyces cerevisiae
1023.9	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Y217F	Saccharomyces cerevisiae
1979	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, mutant Q215A	Saccharomyces cerevisiae
11875	-	5-Fluoroorotidine 5'-phosphate	pH 7.1, 25°C, wild-type enzyme	Saccharomyces cerevisiae

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Release 2023.1 (January 2023)