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Literature summary for 4.1.1.23 extracted from
- Orotidine 5'-monophosphate decarboxylase probing the limits of the possible for enzyme catalysis (2018), Acc. Chem. Res., 51, 960-969 .
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| 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 | Saccharomyces cerevisiae | |
| 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 | Saccharomyces cerevisiae |  |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli | Saccharomyces cerevisiae |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| Q215A | site-directed mutagenesis | Saccharomyces cerevisiae |
| 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 | Saccharomyces cerevisiae |
| Q215A/R235A | site-directed mutagenesis, no dianion activation | Saccharomyces cerevisiae |
| Q215A/Y217F/R235A | site-directed mutagenesis, no dianion activation | Saccharomyces cerevisiae |
| 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 | Saccharomyces cerevisiae |
| 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 | Saccharomyces cerevisiae |
| S154A | site-directed mutagenesis | Saccharomyces cerevisiae |
| S154A/Q215A | site-directed mutagenesis | Saccharomyces cerevisiae |
| 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 | Saccharomyces cerevisiae |
| Y217F/R235A | site-directed mutagenesis, no dianion activation | Saccharomyces cerevisiae |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | kinetic analysis | 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 |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| 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 | Saccharomyces cerevisiae |
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 | - |
? | |
| 5-fluoroorotate | - |
Saccharomyces cerevisiae | 5-fluorouracil + CO2 | - |
? | |
| 5-fluoroorotate | - |
Saccharomyces cerevisiae ATCC 204508 / S288c | 5-fluorouracil + CO2 | - |
? | |
| 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 | Saccharomyces cerevisiae | ? | - |
? | |
| 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 | 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 |
| URA3 | - |
Saccharomyces cerevisiae |
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