BRENDA - Enzyme Database

Biochemical, kinetic, and spectroscopic characterization of Ruegeria pomeroyi DddW - A mononuclear iron-dependent DMSP lyase

Brummett, A.; Schnicker, N.; Crider, A.; Todd, J.; Dey, M.; PLoS ONE 10, e0127288 (2015)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
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
Commentary
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
Commentary
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]
Commentary
Organism
4.4.1.3
35000
-
dynamic light scattering
Ruegeria pomeroyi
4.4.1.3
36000
-
gel filtration
Ruegeria pomeroyi
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
4.4.1.3
Ruegeria pomeroyi
Q5LW89
-
-
4.4.1.3
Ruegeria pomeroyi DSM 15171
Q5LW89
-
-
Purification (Commentary)
EC Number
Commentary
Organism
4.4.1.3
recombinant protein
Ruegeria pomeroyi
Specific Activity [micromol/min/mg]
EC Number
Specific Activity Minimum [Ámol/min/mg]
Specific Activity Maximum [Ámol/min/mg]
Commentary
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
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4.4.1.3
beta-dimethylsulfoniopropanoate
-
749057
Ruegeria pomeroyi
dimethylsulfide + acrylate
-
-
-
?
4.4.1.3
beta-dimethylsulfoniopropanoate
-
749057
Ruegeria pomeroyi DSM 15171
dimethylsulfide + acrylate
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
4.4.1.3
dimer
2 * 18000-22000, SDS-PAGE, 2 * 18000, calculated from sequence, His-tagged recombinant protein
Ruegeria pomeroyi
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
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
Commentary
Organism
4.4.1.3
8
-
-
Ruegeria pomeroyi
Cloned(Commentary) (protein specific)
EC Number
Commentary
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] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
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 (protein specific)
EC Number
Metals/Ions
Commentary
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] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
4.4.1.3
35000
-
dynamic light scattering
Ruegeria pomeroyi
4.4.1.3
36000
-
gel filtration
Ruegeria pomeroyi
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
4.4.1.3
recombinant protein
Ruegeria pomeroyi
Specific Activity [micromol/min/mg] (protein specific)
EC Number
Specific Activity Minimum [Ámol/min/mg]
Specific Activity Maximum [Ámol/min/mg]
Commentary
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) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4.4.1.3
beta-dimethylsulfoniopropanoate
-
749057
Ruegeria pomeroyi
dimethylsulfide + acrylate
-
-
-
?
4.4.1.3
beta-dimethylsulfoniopropanoate
-
749057
Ruegeria pomeroyi DSM 15171
dimethylsulfide + acrylate
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
4.4.1.3
dimer
2 * 18000-22000, SDS-PAGE, 2 * 18000, calculated from sequence, His-tagged recombinant protein
Ruegeria pomeroyi
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
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 (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
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
Commentary
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
KCat/KM [mM/s] (protein specific)
EC Number
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
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