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Literature summary for 4.1.1.2 extracted from
- Oxalate decarboxylase requires manganese and dioxygen for activity. Overexpression and characterization of Bacillus subtilis YvrK and YoaN (2001), J. Biol. Chem., 276, 43627-43634.
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| additional information | induced by acidic pH and not by oxalate | Bacillus subtilis |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| yoaN gene, overexpression in Escherichia coli BL21(DE3)pLysS | Bacillus subtilis |
| yvrK gene, overexpression in Escherichia coli BL21(DE3)pLysS | Bacillus subtilis |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| Dithionite | 1 mM, complete loss of activity, some irreversible effect | Bacillus subtilis |  |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 15 | - |
oxalate | pH 5, 26°C, recombinant YvrK | Bacillus subtilis | |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| soluble | recombinant YoaN | Bacillus subtilis | - |
- |
| soluble | recombinant YvrK | Bacillus subtilis | - |
- |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mn2+ | specific requirement | Bacillus subtilis | |
| Mn2+ | specific requirement for the correct folding and activity, contains between 0.86 and 1.14 atoms of manganese per subunit, predominantly in the Mn2+ oxidation state, both Mn2+ and O2 are cofactors acting together as a two-electron sink during catalysis | Bacillus subtilis | |
| additional information | not: Fe2+, Cu2+, Ni2+, Co2+, Mg2+, Zn2+ | Bacillus subtilis |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 44000 | - |
6 * 44000, recombinant YvrK, SDS-PAGE | Bacillus subtilis |
| 222000 | - |
recombinant YvrK, nondenaturing PAGE | Bacillus subtilis |
| 254000 | - |
recombinant YvrK, gel filtration | Bacillus subtilis |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| oxalate + H+ | Bacillus subtilis | oxalate-degrading enzyme | formate + CO2 | - |
? | |
| oxalate + H+ | Bacillus subtilis | oxalate-degrading enzyme, may be involved in the elevation of cytoplasmic pH, because the reaction involves the net consumption of a proton | formate + CO2 | - |
? | |
| oxalate + H+ | Bacillus subtilis 168 | oxalate-degrading enzyme | formate + CO2 | - |
? | |
| oxalate + H+ | Bacillus subtilis 168 | oxalate-degrading enzyme, may be involved in the elevation of cytoplasmic pH, because the reaction involves the net consumption of a proton | formate + CO2 | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Bacillus subtilis | O34714 | - |
- |
| Bacillus subtilis | O34767 | - |
- |
| Bacillus subtilis 168 | O34714 | - |
- |
| Bacillus subtilis 168 | O34767 | - |
- |
Oxidation Stability
| Oxidation Stability | Organism |
|---|---|
| YvrK is occasionally prone to oxidation during the latter stages of the purification resulting in its dimerization, which is prevented by dithiothreitol | Bacillus subtilis |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant YvrK, 20.7fold | Bacillus subtilis |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| oxalate = formate + CO2 | mechanism | Bacillus subtilis |
Specific Activity [micromol/min/mg]
| Specific Activity Minimum [µmol/min/mg] | Specific Activity Maximum [µmol/min/mg] | Comment | Organism |
|---|---|---|---|
| 65 | - |
pH 5, 26°C, recombinant YvrK | Bacillus subtilis |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | enzyme catalyzes minor side reactions: oxalate oxidation to produce H2O2 and oxalate-dependent, H2O2-independent dye oxidations | Bacillus subtilis | ? | - |
? | |
| additional information | enzyme catalyzes minor side reactions: oxalate oxidation to produce H2O2 and oxalate-dependent, H2O2-independent dye oxidations, at less than 1% of the oxalate decarboxylation rate | Bacillus subtilis | ? | - |
? | |
| additional information | enzyme catalyzes minor side reactions: oxalate oxidation to produce H2O2 and oxalate-dependent, H2O2-independent dye oxidations | Bacillus subtilis 168 | ? | - |
? | |
| additional information | enzyme catalyzes minor side reactions: oxalate oxidation to produce H2O2 and oxalate-dependent, H2O2-independent dye oxidations, at less than 1% of the oxalate decarboxylation rate | Bacillus subtilis 168 | ? | - |
? | |
| oxalate + H+ | contains two potential active sites per subunit | Bacillus subtilis | formate + CO2 | - |
? | |
| oxalate + H+ | enzyme structure, YvrK possesses two potential active sites per subunit, but only one could be fully occupied by manganese, mechanism, catalytic cycle | Bacillus subtilis | formate + CO2 | - |
? | |
| oxalate + H+ | oxalate-degrading enzyme | Bacillus subtilis | formate + CO2 | - |
? | |
| oxalate + H+ | oxalate-degrading enzyme, may be involved in the elevation of cytoplasmic pH, because the reaction involves the net consumption of a proton | Bacillus subtilis | formate + CO2 | - |
? | |
| oxalate + H+ | contains two potential active sites per subunit | Bacillus subtilis 168 | formate + CO2 | - |
? | |
| oxalate + H+ | enzyme structure, YvrK possesses two potential active sites per subunit, but only one could be fully occupied by manganese, mechanism, catalytic cycle | Bacillus subtilis 168 | formate + CO2 | - |
? | |
| oxalate + H+ | oxalate-degrading enzyme | Bacillus subtilis 168 | formate + CO2 | - |
? | |
| oxalate + H+ | oxalate-degrading enzyme, may be involved in the elevation of cytoplasmic pH, because the reaction involves the net consumption of a proton | Bacillus subtilis 168 | formate + CO2 | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| hexamer | - |
Bacillus subtilis |
| hexamer | 6 * 44000, recombinant YvrK, SDS-PAGE | Bacillus subtilis |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| More | belongs to the cupin superfamily, bicupin | Bacillus subtilis |
| YoaN | - |
Bacillus subtilis |
| YvrK | - |
Bacillus subtilis |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 26 | - |
assay at | Bacillus subtilis |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 54 | - |
oxalate | pH 5, 26°C, recombinant YvrK | Bacillus subtilis | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 5 | - |
assay at | Bacillus subtilis |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| O2 | requirement, both Mn2+ and O2 are cofactors acting together as a two-electron sink during catalysis | Bacillus subtilis | |
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