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Literature summary for 4.1.1.23 extracted from

  • 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 (2014), J. Am. Chem. Soc., 136, 10156-10165 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 4.1.1.23

Inhibitors

Inhibitors Comment Organism Structure
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 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 substrate orotidine 5'-phosphate Saccharomyces cerevisiae
0.0014
-
 orotidine 5'-phosphate pH 7.1, 25°C, wild-type enzyme Saccharomyces cerevisiae
0.092
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A Saccharomyces cerevisiae
0.11
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant R235A Saccharomyces cerevisiae
0.11
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant Y217F Saccharomyces cerevisiae
0.29 1.4 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A/Y271F Saccharomyces cerevisiae
0.35 1.4 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A/R235A Saccharomyces cerevisiae
2.2 12.9 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A/Y217F/R235A Saccharomyces cerevisiae
6.1 27.1 orotidine 5'-phosphate pH 7.1, 25°C, mutant Y217F/R235A 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
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1-(beta-D-erythrofuranosyl)-5-fluoroorotate
-
 Saccharomyces cerevisiae 1-(beta-D-erythrofuranosyl)-5-fluorouracil + CO2
-
 ?
1-(beta-D-erythrofuranosyl)-5-fluoroorotate
-
 Saccharomyces cerevisiae ATCC 204508 / S288c 1-(beta-D-erythrofuranosyl)-5-fluorouracil + CO2
-
 ?
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
-
 ?
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

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
0.00048
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A/Y217F/R235A Saccharomyces cerevisiae
0.11
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant Y217F/R235A Saccharomyces cerevisiae
0.19 0.2 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A/R235A Saccharomyces cerevisiae
1
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant R235A Saccharomyces cerevisiae
4.85
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A/Y271F Saccharomyces cerevisiae
15
-
 orotidine 5'-phosphate pH 7.1, 25°C, wild-type enzyme Saccharomyces cerevisiae
20
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant Y217F Saccharomyces cerevisiae
24
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A 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 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 Saccharomyces cerevisiae

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.000037 0.00022 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A/Y217F/R235A Saccharomyces cerevisiae
0.0041 0.018 orotidine 5'-phosphate pH 7.1, 25°C, mutant Y217F/R235A Saccharomyces cerevisiae
0.014 0.054 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A/R235A Saccharomyces cerevisiae
0.91
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant R235A Saccharomyces cerevisiae
3.4 17 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A/Y271F Saccharomyces cerevisiae
180
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant Y217F Saccharomyces cerevisiae
260
-
 orotidine 5'-phosphate pH 7.1, 25°C, mutant Q215A Saccharomyces cerevisiae
11000
-
 orotidine 5'-phosphate pH 7.1, 25°C, wild-type enzyme Saccharomyces cerevisiae