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Literature summary extracted from

  • Brummett, A.; Schnicker, N.; Crider, A.; Todd, J.; Dey, M.
    Biochemical, kinetic, and spectroscopic characterization of Ruegeria pomeroyi DddW - A mononuclear iron-dependent DMSP lyase (2015), PLoS ONE, 10, e0127288 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.4.1.3 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]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.4.1.3 4.5
-
 beta-dimethylsulfoniopropanoate presence of Mn2+, pH 8.0, temperature not specified in the publication Ruegeria pomeroyi
4.4.1.3 8.68
-
 beta-dimethylsulfoniopropanoate presence of Fe2+, pH 8.0, temperature not specified in the publication Ruegeria pomeroyi

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.4.1.3 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
4.4.1.3 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
4.4.1.3 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
4.4.1.3 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
4.4.1.3 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]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
4.4.1.3 35000
-
 dynamic light scattering Ruegeria pomeroyi
4.4.1.3 36000
-
 gel filtration Ruegeria pomeroyi

Organism

EC Number Organism UniProt Comment Textmining
4.4.1.3 Ruegeria pomeroyi Q5LW89
-
-
4.4.1.3 Ruegeria pomeroyi DSM 15171 Q5LW89
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.4.1.3 recombinant protein Ruegeria pomeroyi

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
4.4.1.3 1.02
-
 presence of Mn2+, pH 8.0, temperature not specified in the publication Ruegeria pomeroyi
4.4.1.3 1.08
-
 presence of Fe2+, pH 8.0, temperature not specified in the publication Ruegeria pomeroyi

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.4.1.3 beta-dimethylsulfoniopropanoate
-
 Ruegeria pomeroyi dimethylsulfide + acrylate
-
 ?
4.4.1.3 beta-dimethylsulfoniopropanoate
-
 Ruegeria pomeroyi DSM 15171 dimethylsulfide + acrylate
-
 ?

Subunits

EC Number Subunits Comment Organism
4.4.1.3 dimer 2 * 18000-22000, SDS-PAGE, 2 * 18000, calculated from sequence, His-tagged recombinant protein Ruegeria pomeroyi

Synonyms

EC Number Synonyms Comment Organism
4.4.1.3 DddW
-
 Ruegeria pomeroyi

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.4.1.3 17.33
-
 beta-dimethylsulfoniopropanoate presence of Mn2+, pH 8.0, temperature not specified in the publication Ruegeria pomeroyi
4.4.1.3 18.25
-
 beta-dimethylsulfoniopropanoate presence of Fe2+, pH 8.0, temperature not specified in the publication Ruegeria pomeroyi

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.4.1.3 8
-
-
 Ruegeria pomeroyi

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
4.4.1.3 2.1
-
 beta-dimethylsulfoniopropanoate presence of Fe2+, pH 8.0, temperature not specified in the publication Ruegeria pomeroyi
4.4.1.3 3.85
-
 beta-dimethylsulfoniopropanoate presence of Mn2+, pH 8.0, temperature not specified in the publication Ruegeria pomeroyi