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Literature summary extracted from
- Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria (2011), Nature, 473, 208-211.
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 6.2.1.44 | the dmdB gene is cloned into the pET101 expression vector and expressed in Escherichia coli, and the recombinant Escherichia coli strain possesses 3-(methylthio)propionyl-CoA ligase activity, whereas the host strain alone does not | Ruegeria pomeroyi |
Molecular Weight [Da]
| EC Number | Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|---|
| 1.3.99.41 | 62854 | - |
x * 62854, calculated from sequence | Ruegeria pomeroyi |
| 6.2.1.44 | 59066 | - |
x * 59066, calculated from sequence | Ruegeria pomeroyi |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.3.99.41 | 3-(methylthio)propionyl-CoA + acceptor | Ruegeria pomeroyi | once released from phytoplankton, marine bacteria degrade dimethylsulfoniopropionate by either the cleavage pathway (to form the volatile gas dimethylsulfide) or the demethylation pathway (yielding methanethiol, which is readily assimilated or oxidized). The enzyme DmdC, 3-(methylthio)propionyl-CoA dehydrogenase, catalyzes the first step in the demethylation pathway | (2E)-3-(methylthio)prop-2-enoyl-CoA + reduced acceptor | - |
? |  |
| 4.2.1.155 | 3-(methylthio)acryloyl-CoA + 2 H2O | Ruegeria pomeroyi | the enzyme involved in the degradation of 3-(dimethylsulfonio)propanoate, an osmolyte produced by marine phytoplankton | acetaldehyde + methanethiol + CoA + CO2 | - |
? | |
| 4.2.1.155 | 3-(methylthio)acryloyl-CoA + 2 H2O | Ruegeria pomeroyi DSM 15171 | the enzyme involved in the degradation of 3-(dimethylsulfonio)propanoate, an osmolyte produced by marine phytoplankton | acetaldehyde + methanethiol + CoA + CO2 | - |
? | |
| 6.2.1.44 | ATP + 3-(methylthio)propanoate + CoA | Ruegeria pomeroyi | degradation 3-(methylthio)propanoate, the first product in 3-(dimethylsulfonio)propanoate degradation. 3-(Dimethylsulfonio)propanoate is an osmolyte of many marine algae and certain plants. The global importance of dimethylsulfoniopropionate lies in its availability as a carbon and sulfur source for marine microorganisms and as a precursor of the gas dimethylsulfide, the oceanic emission of which leads to the formation of cloud condensation nuclei and promotion of solar radiation backscatter. Two competing pathways exist for the bacterial catabolism of 3-(dimethylsulfonio)propanoate, one releasing dimethylsulphide and the other releasing methanethiol | AMP + diphosphate + 3-(methylthio)propionyl-CoA | - |
? | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 1.3.99.41 | Ruegeria pomeroyi | Q5LLW7 | - |
- |
| 4.2.1.155 | Ruegeria pomeroyi | Q5LLW6 | - |
- |
| 4.2.1.155 | Ruegeria pomeroyi DSM 15171 | Q5LLW6 | - |
- |
| 6.2.1.44 | Ruegeria pomeroyi | Q5LRT0 | - |
- |
Purification (Commentary)
| EC Number | Purification (Comment) | Organism |
|---|---|---|
| 4.2.1.155 | - |
Ruegeria pomeroyi |
| 6.2.1.44 | - |
Ruegeria pomeroyi |
Specific Activity [micromol/min/mg]
| EC Number | Specific Activity Minimum [µmol/min/mg] | Specific Activity Maximum [µmol/min/mg] | Comment | Organism |
|---|---|---|---|---|
| 1.3.99.41 | 1.23 | - |
chemostat, pH and temperature not specified in the publication | Ruegeria pomeroyi |
| 6.2.1.44 | 0.118 | - |
chemostat, pH and temperature not specified in the publication | Ruegeria pomeroyi |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.3.99.41 | 3-(methylthio)propionyl-CoA + acceptor | - |
Ruegeria pomeroyi | (2E)-3-(methylthio)prop-2-enoyl-CoA + reduced acceptor | - |
? | |
| 1.3.99.41 | 3-(methylthio)propionyl-CoA + acceptor | once released from phytoplankton, marine bacteria degrade dimethylsulfoniopropionate by either the cleavage pathway (to form the volatile gas dimethylsulfide) or the demethylation pathway (yielding methanethiol, which is readily assimilated or oxidized). The enzyme DmdC, 3-(methylthio)propionyl-CoA dehydrogenase, catalyzes the first step in the demethylation pathway | Ruegeria pomeroyi | (2E)-3-(methylthio)prop-2-enoyl-CoA + reduced acceptor | - |
? | |
| 4.2.1.155 | 3-(methylthio)acryloyl-CoA + 2 H2O | the enzyme involved in the degradation of 3-(dimethylsulfonio)propanoate, an osmolyte produced by marine phytoplankton | Ruegeria pomeroyi | acetaldehyde + methanethiol + CoA + CO2 | - |
? | |
| 4.2.1.155 | 3-(methylthio)acryloyl-CoA + 2 H2O | 3-(methylthio)acryloyl-CoA i.e. 3-(methylthio)prop-2-enoyl-CoA | Ruegeria pomeroyi | acetaldehyde + methanethiol + CoA + CO2 | - |
? | |
| 4.2.1.155 | 3-(methylthio)acryloyl-CoA + 2 H2O | the enzyme involved in the degradation of 3-(dimethylsulfonio)propanoate, an osmolyte produced by marine phytoplankton | Ruegeria pomeroyi DSM 15171 | acetaldehyde + methanethiol + CoA + CO2 | - |
? | |
| 4.2.1.155 | 3-(methylthio)acryloyl-CoA + 2 H2O | 3-(methylthio)acryloyl-CoA i.e. 3-(methylthio)prop-2-enoyl-CoA | Ruegeria pomeroyi DSM 15171 | acetaldehyde + methanethiol + CoA + CO2 | - |
? | |
| 6.2.1.44 | ATP + 3-(methylthio)propanoate + CoA | - |
Ruegeria pomeroyi | AMP + diphosphate + 3-(methylthio)propionyl-CoA | - |
? | |
| 6.2.1.44 | ATP + 3-(methylthio)propanoate + CoA | degradation 3-(methylthio)propanoate, the first product in 3-(dimethylsulfonio)propanoate degradation. 3-(Dimethylsulfonio)propanoate is an osmolyte of many marine algae and certain plants. The global importance of dimethylsulfoniopropionate lies in its availability as a carbon and sulfur source for marine microorganisms and as a precursor of the gas dimethylsulfide, the oceanic emission of which leads to the formation of cloud condensation nuclei and promotion of solar radiation backscatter. Two competing pathways exist for the bacterial catabolism of 3-(dimethylsulfonio)propanoate, one releasing dimethylsulphide and the other releasing methanethiol | Ruegeria pomeroyi | AMP + diphosphate + 3-(methylthio)propionyl-CoA | - |
? | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 1.3.99.41 | ? | x * 62854, calculated from sequence | Ruegeria pomeroyi |
| 6.2.1.44 | ? | x * 59066, calculated from sequence | Ruegeria pomeroyi |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 1.3.99.41 | 3-methylmercaptopropionyl-CoA dehydrogenase | - |
Ruegeria pomeroyi |
| 1.3.99.41 | dmdC | - |
Ruegeria pomeroyi |
| 1.3.99.41 | SPO3804 | locus name | Ruegeria pomeroyi |
| 4.2.1.155 | MTA-CoA hydratase | - |
Ruegeria pomeroyi |
| 4.2.1.155 | SPO3805 | locus name | Ruegeria pomeroyi |
| 6.2.1.44 | DmdB | - |
Ruegeria pomeroyi |
| 6.2.1.44 | MMPA-CoA ligase | - |
Ruegeria pomeroyi |
| 6.2.1.44 | SPO2045 | - |
Ruegeria pomeroyi |
Expression
| EC Number | Organism | Comment | Expression |
|---|---|---|---|
| 1.3.99.41 | Ruegeria pomeroyi | the amount of transcripts for dmdB, dmdC and dmdD increases during growth of wild-type enzyme on methylmercaptopropionate or 3-(dimethylsulphonio)propanoate, as expected if the pathway is required for 3-(methylthio)propanoate metabolism. Following growth with 3-(dimethylsulphonio)propanoate, the levels of DmdC and DmdD activity in the deletion mutant dmdC are greatly reduced | up |
| 6.2.1.44 | Ruegeria pomeroyi | the amount of transcripts for dmdB, dmdC and dmdD increases during growth of wild-type enzyme on 3-(methylthio)propanoate or 3-(dimethylsulphonio)propanoate, as expected if the pathway is required for 3-(methylthio)propanoate metabolism | up |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 1.3.99.41 | malfunction | a dmdC2 mutant (SPO3804::Tn5) can not grow on 3-(methylthio)propanoate as the sole source of carbon, indicating that this pathway is essential for growth on 3-(methylthio)propanoate. In contrast, the mutant grows similarly to wild-type with 3-(dimethylsulphonio)propanoate, indicating that the cleavage pathway, initiated by DddQ or DddP13, remains capable of supporting growth | Ruegeria pomeroyi |
| 1.3.99.41 | metabolism | in extracts of chemostat-grown cells the levels of DmdB, DmdC and DmdD activities exceed the minimum level, 57 nmol/min*mg of protein, necessary to support growth. The amount of transcripts for dmdB, dmdC and dmdD increase during growth on 3-(methylthio)propanoate or 3-(dimethylsulphonio)propanoate, as expected if the pathway is required for 3-(methylthio)propanoate metabolism | Ruegeria pomeroyi |
| 4.2.1.155 | malfunction | a dmdD (SPO3805::tet) mutant fails to grow with 3-methylmercaptopropionate, and growth on dimethylsulphoniopropionate is severely inhibited | Ruegeria pomeroyi |
| 4.2.1.155 | metabolism | the enzyme is involved in the degradation of 3-(dimethylsulfonio)propanoate, an osmolyte produced by marine phytoplankton. The transcript for dmdD increases during growth on methylmercaptopropionate or dimethylsulphoniopropionate | Ruegeria pomeroyi |
| 6.2.1.44 | malfunction | growth of a dmdB mutant (SPO2045::tet) is somewhat delayed during growth on 3-(methylthio)propionate. Following growth with 3-(dimethylsulphonio)propanoate, the DmdB activity is reduced by only 40% compared to the wild-type | Ruegeria pomeroyi |
| 6.2.1.44 | metabolism | in extracts of chemostat-grown cells the levels of DmdB, DmdC and DmdD activities exceed the minimum level, 57 nmol/min* mg of protein, necessary to support growth. The amount of transcripts for dmdB, dmdC and dmdD increased during growth on 3-(methylthio)propanoate or 3-(dimethylsulphonio)propanoate, as expected if the pathway is required for methylmercaptopropionate metabolism | Ruegeria pomeroyi |
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