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Literature summary for 2.1.1.269 extracted from
- Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi (2008), J. Bacteriol., 190, 8018-8024.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
- |
Candidatus Pelagibacter ubique |
- |
Ruegeria pomeroyi |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| 3-(methylthio)propanoate | - |
Candidatus Pelagibacter ubique |  |
| dimethylsulfoniobutanoate | substrate analog, weak inhibitor | Candidatus Pelagibacter ubique | |
| dimethylsulfoniopentanoate | substrate analog, weak inhibitor | Candidatus Pelagibacter ubique | |
| methylmercaptopropionate | product inhibition | Candidatus Pelagibacter ubique | |
| MgCl2 | 100 mM, 20% inhibition | Candidatus Pelagibacter ubique | |
| MgCl2 | 100 mM, 20% inhibition | Ruegeria pomeroyi | |
| additional information | not inhibitory: 400 mM of (NH4)2SO4, K2HPO4, MgSO4, Na-acetate, NaCl, and KCl | Candidatus Pelagibacter ubique | |
| additional information | not inhibitory: 400 mM of (NH4)2SO4, K2HPO4, MgSO4, Na-acetate, NaCl, and KCl | Ruegeria pomeroyi |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.21 | - |
tetrahydrofolate | pH 7.5, temperature not specified in the publication | Ruegeria pomeroyi | |
| 0.29 | - |
tetrahydrofolate | pH 7.5, temperature not specified in the publication | Candidatus Pelagibacter ubique | |
| 5.4 | - |
dimethylsulfoniopropionate | - |
Ruegeria pomeroyi | |
| 5.4 | - |
3-(S,S-dimethylsulfonio)propanoate | pH 7.5, temperature not specified in the publication | Ruegeria pomeroyi | |
| 8.6 | - |
dimethylsulfoniopropionate | in cell extracts, similar to that of purified recombinant DmdA | Ruegeria pomeroyi | |
| 13.2 | - |
2-(dimethylsulfonio)propanoate | - |
Candidatus Pelagibacter ubique | |
| 13.2 | - |
3-(S,S-dimethylsulfonio)propanoate | pH 7.5, temperature not specified in the publication | Candidatus Pelagibacter ubique | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 38500 | - |
SDS-PAGE | Candidatus Pelagibacter ubique |
| 38500 | - |
2 * 38500, SDS-PAGE | Candidatus Pelagibacter ubique |
| 38500 | - |
2 * 38500, SDS-PAGE | Ruegeria pomeroyi |
| 68000 | - |
PAGE | Candidatus Pelagibacter ubique |
| 68000 | - |
PAGE | Ruegeria pomeroyi |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Candidatus Pelagibacter ubique | - |
HTCC1062 | - |
| Candidatus Pelagibacter ubique | Q4FP21 | - |
- |
| Candidatus Pelagibacter ubique HTCC1062 | - |
HTCC1062 | - |
| Candidatus Pelagibacter ubique HTCC1062 | Q4FP21 | - |
- |
| Ruegeria pomeroyi | Q5LS57 | - |
- |
| Ruegeria pomeroyi | Q5LS57 | DSS-3 | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| anion-exchange, hydrophobic interaction, and hydroxyapatite chromatographies | Candidatus Pelagibacter ubique |
| anion-exchange, hydrophobic interaction, and hydroxyapatite chromatographies | Ruegeria pomeroyi |
| recombinant protein | Candidatus Pelagibacter ubique |
| recombinant protein | Ruegeria pomeroyi |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 2-(dimethylsulfonio)propanoate + tetrahydrofolate | enzyme exhibits strict substrate specificity for 2-(dimethylsulfonio)propanoate | Candidatus Pelagibacter ubique | 2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
| 2-(dimethylsulfonio)propanoate + tetrahydrofolate | enzyme exhibits strict substrate specificity for 2-(dimethylsulfonio)propanoate | Ruegeria pomeroyi | 2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
| 2-(dimethylsulfonio)propanoate + tetrahydrofolate | enzyme exhibits strict substrate specificity for 2-(dimethylsulfonio)propanoate | Candidatus Pelagibacter ubique HTCC1062 | 2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
| 2-(dimethylsulfonio)propanoate + tetrahydrofolate | - |
Candidatus Pelagibacter ubique | 2-(methylthio)propanoate + 5-methyltetrahydrofolate | - |
r | |
| 2-(dimethylsulfonio)propanoate + tetrahydrofolate | - |
Candidatus Pelagibacter ubique HTCC1062 | 2-(methylthio)propanoate + 5-methyltetrahydrofolate | - |
r | |
| 3-(S,S-dimethylsulfonio)propanoate + tetrahydrofolate | - |
Candidatus Pelagibacter ubique | 3-(methylthio)propanoate + 5-methyltetrahydrofolate | - |
? | |
| 3-(S,S-dimethylsulfonio)propanoate + tetrahydrofolate | - |
Ruegeria pomeroyi | 3-(methylthio)propanoate + 5-methyltetrahydrofolate | - |
? | |
| 3-(S,S-dimethylsulfonio)propanoate + tetrahydrofolate | - |
Candidatus Pelagibacter ubique HTCC1062 | 3-(methylthio)propanoate + 5-methyltetrahydrofolate | - |
? | |
| additional information | no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity is found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate | Candidatus Pelagibacter ubique | ? | - |
? | |
| additional information | no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity is found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate | Ruegeria pomeroyi | ? | - |
? | |
| additional information | strict substrate specificity for dimethylsulfoniopropionate. No detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate and less than 1% activity with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate | Ruegeria pomeroyi | ? | - |
? | |
| additional information | strict substrate specificity for dimethylsulfoniopropionate. No detectable demethylase activity with glycine betaine,dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate and less than 1% activity with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate | Candidatus Pelagibacter ubique | ? | - |
? | |
| additional information | no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity is found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate | Candidatus Pelagibacter ubique HTCC1062 | ? | - |
? | |
| additional information | strict substrate specificity for dimethylsulfoniopropionate. No detectable demethylase activity with glycine betaine,dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate and less than 1% activity with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate | Candidatus Pelagibacter ubique HTCC1062 | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| dimer | 2 * 38500, SDS-PAGE | Candidatus Pelagibacter ubique |
| dimer | 2 * 38500, SDS-PAGE | Ruegeria pomeroyi |
| dimer | under nondenaturing conditions, MW is 68000 Da, suggesting that the enzyme is likely to be a dimer | Candidatus Pelagibacter ubique |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| dimethylsulfoniopropionate demethylase | - |
Candidatus Pelagibacter ubique |
| dimethylsulfoniopropionate-dependent demethylase | - |
Candidatus Pelagibacter ubique |
| dimethylsulfoniopropionate-dependent demethylase | - |
Ruegeria pomeroyi |
| dimethylsulfoniumpropionate:tetrahydrofolate S-methyltransferase | - |
Candidatus Pelagibacter ubique |
| DmdA | - |
Candidatus Pelagibacter ubique |
| DmdA | - |
Ruegeria pomeroyi |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 2.4 | - |
dimethylsulfoniopropionate | - |
Ruegeria pomeroyi | |
| 2.4 | - |
3-(S,S-dimethylsulfonio)propanoate | pH 7.5, temperature not specified in the publication | Ruegeria pomeroyi | |
| 8.1 | - |
2-(dimethylsulfonio)propanoate | - |
Candidatus Pelagibacter ubique | |
| 8.1 | - |
3-(S,S-dimethylsulfonio)propanoate | pH 7.5, temperature not specified in the publication | Candidatus Pelagibacter ubique | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7 | 8 | maximum activity is observed at pH 7.0 to 8.0 | Candidatus Pelagibacter ubique |
| 7 | 8 | maximum activity is observed at pH 7.0 to 8.0 | Ruegeria pomeroyi |
| 7 | 8 | enzyme is more active in HEPES buffer than in MOPS or Tris-HCl buffer at the same pH | Candidatus Pelagibacter ubique |
| 7 | 8 | enzyme is more active in HEPES than in MOPS buffer, but the activities in HEPES and Tris-HCl buffers are the same | Ruegeria pomeroyi |
pH Range
| pH Minimum | pH Maximum | Comment | Organism |
|---|---|---|---|
| 6 | 8.8 | more than 50% of maximum activity within | Ruegeria pomeroyi |
| 6 | 8.8 | maximum activity is observed at pH 7.0 to 8.0, about 50% activity at pH 6.0 and 8.8 | Ruegeria pomeroyi |
| 6.5 | 8.3 | more than 50% of maximum activity within | Candidatus Pelagibacter ubique |
| 6.5 | 8.3 | maximum activity is observed at pH 7.0 to 8.0, about 50% activity at pH 6.5 and 8.3 | Candidatus Pelagibacter ubique |
Ki Value [mM]
| Ki Value [mM] | Ki Value maximum [mM] | Inhibitor | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 2.1 | - |
methylmercaptopropionate | noncompetitive inhibition, product inhibition | Candidatus Pelagibacter ubique | |
| 2.1 | - |
3-(methylthio)propanoate | pH 7.5, temperature not specified in the publication | Candidatus Pelagibacter ubique | |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.45 | - |
3-(S,S-dimethylsulfonio)propanoate | pH 7.5, temperature not specified in the publication | Ruegeria pomeroyi | |
| 0.618 | - |
3-(S,S-dimethylsulfonio)propanoate | pH 7.5, temperature not specified in the publication | Candidatus Pelagibacter ubique | |
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