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Literature summary for 4.4.1.3 extracted from
- Biochemical, kinetic, and spectroscopic characterization of Ruegeria pomeroyi DddW - A mononuclear iron-dependent DMSP lyase (2015), PLoS ONE, 10, e0127288 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| expression in Escherichia coli. Expression of recombinant DddW in minimal media in the absence of any added metal ion leads to the formation of insoluble protein | Ruegeria pomeroyi |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 4.5 | - |
beta-dimethylsulfoniopropanoate | presence of Mn2+, pH 8.0, temperature not specified in the publication | Ruegeria pomeroyi |  |
| 8.68 | - |
beta-dimethylsulfoniopropanoate | presence of Fe2+, pH 8.0, temperature not specified in the publication | Ruegeria pomeroyi | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Cobalt | DddW has the highest affinity for binding Fe(II) at 5 nM, followed by Co(II), Ni(II), and Cu(II) at about 1-3 microM | Ruegeria pomeroyi | |
| copper | DddW has the highest affinity for binding Fe(II) at 5 nM, followed by Co(II), Ni(II), and Cu(II) at about 1-3 microM | Ruegeria pomeroyi | |
| Iron | the as-isolated enzyme contains 0.2-0.4 equivalents of bound iron. DddW has the highest affinity for binding Fe(II) at 5 nM, followed by Co(II), Ni(II), and Cu(II) at about 1-3 microM, with Mn(II) and Fe(III) exhibiting weaker binding affinities. The presence of Fe(II) or Mn(II) elicits an about 40fold increase in DddW lyase activity compared to the apo-enzyme | Ruegeria pomeroyi | |
| Manganese | the presence of Fe(II) or Mn(II) elicits an about 40fold increase in DddW lyase activity compared to the apo-enzyme | Ruegeria pomeroyi | |
| Nickel | DddW has the highest affinity for binding Fe(II) at 5 nM, followed by Co(II), Ni(II), and Cu(II) at about 1-3 microM | Ruegeria pomeroyi | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 35000 | - |
dynamic light scattering | Ruegeria pomeroyi |
| 36000 | - |
gel filtration | Ruegeria pomeroyi |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Ruegeria pomeroyi | Q5LW89 | - |
- |
| Ruegeria pomeroyi DSM 15171 | Q5LW89 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant protein | Ruegeria pomeroyi |
Specific Activity [micromol/min/mg]
| Specific Activity Minimum [µmol/min/mg] | Specific Activity Maximum [µmol/min/mg] | Comment | Organism |
|---|---|---|---|
| 1.02 | - |
presence of Mn2+, pH 8.0, temperature not specified in the publication | Ruegeria pomeroyi |
| 1.08 | - |
presence of Fe2+, pH 8.0, temperature not specified in the publication | Ruegeria pomeroyi |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| beta-dimethylsulfoniopropanoate | - |
Ruegeria pomeroyi | dimethylsulfide + acrylate | - |
? | |
| beta-dimethylsulfoniopropanoate | - |
Ruegeria pomeroyi DSM 15171 | dimethylsulfide + acrylate | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| dimer | 2 * 18000-22000, SDS-PAGE, 2 * 18000, calculated from sequence, His-tagged recombinant protein | Ruegeria pomeroyi |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| DddW | - |
Ruegeria pomeroyi |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 17.33 | - |
beta-dimethylsulfoniopropanoate | presence of Mn2+, pH 8.0, temperature not specified in the publication | Ruegeria pomeroyi | |
| 18.25 | - |
beta-dimethylsulfoniopropanoate | presence of Fe2+, pH 8.0, temperature not specified in the publication | Ruegeria pomeroyi | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 8 | - |
- |
Ruegeria pomeroyi |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 2.1 | - |
beta-dimethylsulfoniopropanoate | presence of Fe2+, pH 8.0, temperature not specified in the publication | Ruegeria pomeroyi | |
| 3.85 | - |
beta-dimethylsulfoniopropanoate | presence of Mn2+, pH 8.0, temperature not specified in the publication | Ruegeria pomeroyi | |
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