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Literature summary for 2.1.1.269 extracted from
- Assay and analysis of dimethylsulfoniopropionate demethylase (2018), Methods Enzymol., 605, 325-333 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene dmdA, functional recombinant expression in Escherichia coli | Candidatus Pelagibacter ubique |
| gene dmdA, functional recombinant expression in Escherichia coli | Ruegeria pomeroyi |
General Stability
| General Stability | Organism |
|---|---|
| salt solutions do not significantly stimulate activity nor are they required for enzyme stability during storage | Candidatus Pelagibacter ubique |
| salt solutions do not significantly stimulate activity nor are they required for enzyme stability during storage | Ruegeria pomeroyi |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 5.4 | - |
S,S-dimethyl-beta-propiothetin | pH 7.5, 30°C, cell extract | Ruegeria pomeroyi |  |
| 13.2 | - |
S,S-dimethyl-beta-propiothetin | pH 7.5, 30°C, cell extract | Candidatus Pelagibacter ubique | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| additional information | salt solutions do not significantly stimulate activity nor are they required for enzyme stability during storage | Candidatus Pelagibacter ubique | |
| additional information | salt solutions do not significantly stimulate activity nor are they required for enzyme stability during storage | Ruegeria pomeroyi |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| S,S-dimethyl-beta-propiothetin + tetrahydrofolate | Candidatus Pelagibacter ubique | - |
3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
| S,S-dimethyl-beta-propiothetin + tetrahydrofolate | Ruegeria pomeroyi | - |
3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
| S,S-dimethyl-beta-propiothetin + tetrahydrofolate | Candidatus Pelagibacter ubique HTCC1062 | - |
3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
| S,S-dimethyl-beta-propiothetin + tetrahydrofolate | Ruegeria pomeroyi DSM 15171 | - |
3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
| S,S-dimethyl-beta-propiothetin + tetrahydrofolate | Ruegeria pomeroyi ATCC 700808 | - |
3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Candidatus Pelagibacter ubique | Q4FP21 | - |
- |
| Candidatus Pelagibacter ubique HTCC1062 | Q4FP21 | - |
- |
| Ruegeria pomeroyi | Q5LS57 | - |
- |
| Ruegeria pomeroyi ATCC 700808 | Q5LS57 | - |
- |
| Ruegeria pomeroyi DSM 15171 | Q5LS57 | - |
- |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| cell culture | - |
Candidatus Pelagibacter ubique | - |
| cell culture | - |
Ruegeria pomeroyi | - |
Storage Stability
| Storage Stability | Organism |
|---|---|
| -20°C, enzyme in cell-free extract, in presence of EDTA and 20% glycerol, several weeks without significant loss of activity | Candidatus Pelagibacter ubique |
| -20°C, enzyme in cell-free extract, in presence of EDTA and 20% glycerol, several weeks without significant loss of activity | Ruegeria pomeroyi |
| 4°C, enzyme in cell-free extract, in presence of EDTA, several weeks without significant loss of activity. Without addition of EDTA, the enzyme loses all activity over the course of several days | Candidatus Pelagibacter ubique |
| 4°C, enzyme in cell-free extract, in presence of EDTA, several weeks without significant loss of activity. Without addition of EDTA, the enzyme loses all activity over the course of several days | Ruegeria pomeroyi |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | assay metod, overview. The substrate THF and product 5-methyl-THF are labile under aerobic conditions, oxidation of THF is irreversible and results in the release of 4-aminobenzoyl glutamate, essentially breaking the molecule in half. Half-life of THF in solution at pH 7.0 is about 40 min. DTT can stabilize THF in solution | Candidatus Pelagibacter ubique | ? | - |
- |
|
| additional information | assay metod, overview. The substrate THF and product 5-methyl-THF are labile under aerobic conditions, oxidation of THF is irreversible and results in the release of 4-aminobenzoyl glutamate, essentially breaking the molecule in half. Half-life of THF in solution at pH 7.0 is about 40 min. DTT can stabilize THF in solution | Ruegeria pomeroyi | ? | - |
- |
|
| additional information | assay metod, overview. The substrate THF and product 5-methyl-THF are labile under aerobic conditions, oxidation of THF is irreversible and results in the release of 4-aminobenzoyl glutamate, essentially breaking the molecule in half. Half-life of THF in solution at pH 7.0 is about 40 min. DTT can stabilize THF in solution | Candidatus Pelagibacter ubique HTCC1062 | ? | - |
- |
|
| additional information | assay metod, overview. The substrate THF and product 5-methyl-THF are labile under aerobic conditions, oxidation of THF is irreversible and results in the release of 4-aminobenzoyl glutamate, essentially breaking the molecule in half. Half-life of THF in solution at pH 7.0 is about 40 min. DTT can stabilize THF in solution | Ruegeria pomeroyi DSM 15171 | ? | - |
- |
|
| additional information | assay metod, overview. The substrate THF and product 5-methyl-THF are labile under aerobic conditions, oxidation of THF is irreversible and results in the release of 4-aminobenzoyl glutamate, essentially breaking the molecule in half. Half-life of THF in solution at pH 7.0 is about 40 min. DTT can stabilize THF in solution | Ruegeria pomeroyi ATCC 700808 | ? | - |
- |
|
| S,S-dimethyl-beta-propiothetin + tetrahydrofolate | - |
Candidatus Pelagibacter ubique | 3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
| S,S-dimethyl-beta-propiothetin + tetrahydrofolate | - |
Ruegeria pomeroyi | 3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
| S,S-dimethyl-beta-propiothetin + tetrahydrofolate | - |
Candidatus Pelagibacter ubique HTCC1062 | 3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
| S,S-dimethyl-beta-propiothetin + tetrahydrofolate | - |
Ruegeria pomeroyi DSM 15171 | 3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
| S,S-dimethyl-beta-propiothetin + tetrahydrofolate | - |
Ruegeria pomeroyi ATCC 700808 | 3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| DmdA | - |
Candidatus Pelagibacter ubique |
| DmdA | - |
Ruegeria pomeroyi |
| DMSP demethylase | - |
Candidatus Pelagibacter ubique |
| DMSP demethylase | - |
Ruegeria pomeroyi |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 30 | - |
assay at | Candidatus Pelagibacter ubique |
| 30 | - |
assay at | Ruegeria pomeroyi |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7.5 | - |
assay at | Candidatus Pelagibacter ubique |
| 7.5 | - |
assay at | Ruegeria pomeroyi |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| tetrahydrofolate | (DMSP) demethylase is a tetrahydrofolate-dependent enzyme | Candidatus Pelagibacter ubique | |
| tetrahydrofolate | (DMSP) demethylase is a tetrahydrofolate-dependent enzyme | Ruegeria pomeroyi | |
Expression
| Organism | Comment | Expression |
|---|---|---|
| Candidatus Pelagibacter ubique | dimethylsulfoniopropionate (DMSP) induces gene dmdA transcription | up |
| Ruegeria pomeroyi | dimethylsulfoniopropionate (DMSP) induces gene dmdA transcription | up |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | though DmdA is homologous to the glycine cleavage T-protein and shares structural similarity, the mechanism of carbon transfer is more similar to S-adenosyl-methionine (SAM)-dependent methyl-transfer enzymes. DmdA catalyzes the transfer of a methyl group to form 5-methyl-THF, which is analogous to SAM-dependent reactions. The gene dmdA is abundant in marine waters | Candidatus Pelagibacter ubique |
| evolution | though DmdA is homologous to the glycine cleavage T-protein and shares structural similarity, the mechanism of carbon transfer is more similar to S-adenosyl-methionine (SAM)-dependent methyl-transfer enzymes. DmdA catalyzes the transfer of a methyl group to form 5-methyl-THF, which is analogous to SAM-dependent reactions. The gene dmdA is abundant in marine waters | Ruegeria pomeroyi |
| physiological function | dimethylsulfoniopropionate (DMSP) demethylase is a tetrahydrofolate-dependent enzyme that initiates the DMSP demethylation pathway in marine bacteria. This enzyme is important for understanding of organic sulfur flux from the oceans because it directs the sulfur from DMSP away from dimethylsulfide | Candidatus Pelagibacter ubique |
| physiological function | dimethylsulfoniopropionate (DMSP) demethylase is a tetrahydrofolate-dependent enzyme that initiates the DMSP demethylation pathway in marine bacteria. This enzyme is important for understanding of organic sulfur flux from the oceans because it directs the sulfur from DMSP away from dimethylsulfide | Ruegeria pomeroyi |
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