BRENDA - Enzyme Database

Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi

Reisch, C.R.; Moran, M.A.; Whitman, W.B.; J. Bacteriol. 190, 8018-8024 (2008)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
2.1.1.269
-
Candidatus Pelagibacter ubique
2.1.1.269
-
Ruegeria pomeroyi
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
2.1.1.269
3-(methylthio)propanoate
-
Candidatus Pelagibacter ubique
2.1.1.269
dimethylsulfoniobutanoate
substrate analog, weak inhibitor
Candidatus Pelagibacter ubique
2.1.1.269
dimethylsulfoniopentanoate
substrate analog, weak inhibitor
Candidatus Pelagibacter ubique
2.1.1.269
methylmercaptopropionate
product inhibition
Candidatus Pelagibacter ubique
2.1.1.269
MgCl2
100 mM, 20% inhibition
Candidatus Pelagibacter ubique
2.1.1.269
MgCl2
100 mM, 20% inhibition
Ruegeria pomeroyi
2.1.1.269
additional information
not inhibitory: 400 mM of (NH4)2SO4, K2HPO4, MgSO4, Na-acetate, NaCl, and KCl
Candidatus Pelagibacter ubique
2.1.1.269
additional information
not inhibitory: 400 mM of (NH4)2SO4, K2HPO4, MgSO4, Na-acetate, NaCl, and KCl
Ruegeria pomeroyi
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
2.1.1.269
0.21
-
tetrahydrofolate
pH 7.5, temperature not specified in the publication
Ruegeria pomeroyi
2.1.1.269
0.29
-
tetrahydrofolate
pH 7.5, temperature not specified in the publication
Candidatus Pelagibacter ubique
2.1.1.269
5.4
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Ruegeria pomeroyi
2.1.1.269
5.4
-
dimethylsulfoniopropionate
-
Ruegeria pomeroyi
2.1.1.269
8.6
-
dimethylsulfoniopropionate
in cell extracts, similar to that of purified recombinant DmdA
Ruegeria pomeroyi
2.1.1.269
13.2
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Candidatus Pelagibacter ubique
2.1.1.269
13.2
-
dimethylsulfoniopropionate
-
Candidatus Pelagibacter ubique
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
2.1.1.269
38500
-
2 * 38500, SDS-PAGE; SDS-PAGE
Candidatus Pelagibacter ubique
2.1.1.269
38500
-
2 * 38500, SDS-PAGE
Ruegeria pomeroyi
2.1.1.269
68000
-
PAGE
Candidatus Pelagibacter ubique
2.1.1.269
68000
-
PAGE
Ruegeria pomeroyi
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
2.1.1.269
Candidatus Pelagibacter ubique
-
HTCC1062
-
2.1.1.269
Candidatus Pelagibacter ubique
Q4FP21
-
-
2.1.1.269
Candidatus Pelagibacter ubique HTCC1062
-
HTCC1062
-
2.1.1.269
Candidatus Pelagibacter ubique HTCC1062
Q4FP21
-
-
2.1.1.269
Ruegeria pomeroyi
Q5LS57
; DSS-3
-
Purification (Commentary)
EC Number
Commentary
Organism
2.1.1.269
anion-exchange, hydrophobic interaction, and hydroxyapatite chromatographies; recombinant protein
Candidatus Pelagibacter ubique
2.1.1.269
anion-exchange, hydrophobic interaction, and hydroxyapatite chromatographies; recombinant protein
Ruegeria pomeroyi
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2.1.1.269
2-(dimethylsulfonio)propanoate + tetrahydrofolate
enzyme exhibits strict substrate specificity for 2-(dimethylsulfonio)propanoate
698600
Candidatus Pelagibacter ubique
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
2-(dimethylsulfonio)propanoate + tetrahydrofolate
enzyme exhibits strict substrate specificity for 2-(dimethylsulfonio)propanoate
698600
Ruegeria pomeroyi
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
2-(dimethylsulfonio)propanoate + tetrahydrofolate
enzyme exhibits strict substrate specificity for 2-(dimethylsulfonio)propanoate
698600
Candidatus Pelagibacter ubique HTCC1062
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
3-(S,S-dimethylsulfonio)propanoate + tetrahydrofolate
-
698600
Candidatus Pelagibacter ubique
3-(methylthio)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
3-(S,S-dimethylsulfonio)propanoate + tetrahydrofolate
-
698600
Ruegeria pomeroyi
3-(methylthio)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
3-(S,S-dimethylsulfonio)propanoate + tetrahydrofolate
-
698600
Candidatus Pelagibacter ubique HTCC1062
3-(methylthio)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
additional information
no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity is found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Candidatus Pelagibacter ubique
?
-
-
-
-
2.1.1.269
additional information
no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity is found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Ruegeria pomeroyi
?
-
-
-
-
2.1.1.269
additional information
strict substrate specificity for dimethylsulfoniopropionate. No detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate and less than 1% activity with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Ruegeria pomeroyi
?
-
-
-
-
2.1.1.269
additional information
strict substrate specificity for dimethylsulfoniopropionate. No detectable demethylase activity with glycine betaine,dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate and less than 1% activity with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Candidatus Pelagibacter ubique
?
-
-
-
-
2.1.1.269
additional information
no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity is found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Candidatus Pelagibacter ubique HTCC1062
?
-
-
-
-
2.1.1.269
additional information
strict substrate specificity for dimethylsulfoniopropionate. No detectable demethylase activity with glycine betaine,dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate and less than 1% activity with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Candidatus Pelagibacter ubique HTCC1062
?
-
-
-
-
Subunits
EC Number
Subunits
Commentary
Organism
2.1.1.269
dimer
2 * 38500, SDS-PAGE; under nondenaturing conditions, MW is 68000 Da, suggesting that the enzyme is likely to be a dimer
Candidatus Pelagibacter ubique
2.1.1.269
dimer
2 * 38500, SDS-PAGE
Ruegeria pomeroyi
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
2.1.1.269
2.4
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Ruegeria pomeroyi
2.1.1.269
2.4
-
dimethylsulfoniopropionate
-
Ruegeria pomeroyi
2.1.1.269
8.1
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Candidatus Pelagibacter ubique
2.1.1.269
8.1
-
dimethylsulfoniopropionate
-
Candidatus Pelagibacter ubique
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
2.1.1.269
7
8
enzyme is more active in HEPES buffer than in MOPS or Tris-HCl buffer at the same pH; maximum activity is observed at pH 7.0 to 8.0
Candidatus Pelagibacter ubique
2.1.1.269
7
8
enzyme is more active in HEPES than in MOPS buffer, but the activities in HEPES and Tris-HCl buffers are the same; maximum activity is observed at pH 7.0 to 8.0
Ruegeria pomeroyi
pH Range
EC Number
pH Minimum
pH Maximum
Commentary
Organism
2.1.1.269
6
8.8
maximum activity is observed at pH 7.0 to 8.0, about 50% activity at pH 6.0 and 8.8; more than 50% of maximum activity within
Ruegeria pomeroyi
2.1.1.269
6.5
8.3
maximum activity is observed at pH 7.0 to 8.0, about 50% activity at pH 6.5 and 8.3; more than 50% of maximum activity within
Candidatus Pelagibacter ubique
Ki Value [mM]
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
2.1.1.269
2.1
-
3-(methylthio)propanoate
pH 7.5, temperature not specified in the publication
Candidatus Pelagibacter ubique
2.1.1.269
2.1
-
methylmercaptopropionate
noncompetitive inhibition, product inhibition
Candidatus Pelagibacter ubique
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
2.1.1.269
-
Candidatus Pelagibacter ubique
2.1.1.269
-
Ruegeria pomeroyi
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
2.1.1.269
3-(methylthio)propanoate
-
Candidatus Pelagibacter ubique
2.1.1.269
dimethylsulfoniobutanoate
substrate analog, weak inhibitor
Candidatus Pelagibacter ubique
2.1.1.269
dimethylsulfoniopentanoate
substrate analog, weak inhibitor
Candidatus Pelagibacter ubique
2.1.1.269
methylmercaptopropionate
product inhibition
Candidatus Pelagibacter ubique
2.1.1.269
MgCl2
100 mM, 20% inhibition
Candidatus Pelagibacter ubique
2.1.1.269
MgCl2
100 mM, 20% inhibition
Ruegeria pomeroyi
2.1.1.269
additional information
not inhibitory: 400 mM of (NH4)2SO4, K2HPO4, MgSO4, Na-acetate, NaCl, and KCl
Candidatus Pelagibacter ubique
2.1.1.269
additional information
not inhibitory: 400 mM of (NH4)2SO4, K2HPO4, MgSO4, Na-acetate, NaCl, and KCl
Ruegeria pomeroyi
Ki Value [mM] (protein specific)
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
2.1.1.269
2.1
-
3-(methylthio)propanoate
pH 7.5, temperature not specified in the publication
Candidatus Pelagibacter ubique
2.1.1.269
2.1
-
methylmercaptopropionate
noncompetitive inhibition, product inhibition
Candidatus Pelagibacter ubique
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
2.1.1.269
0.21
-
tetrahydrofolate
pH 7.5, temperature not specified in the publication
Ruegeria pomeroyi
2.1.1.269
0.29
-
tetrahydrofolate
pH 7.5, temperature not specified in the publication
Candidatus Pelagibacter ubique
2.1.1.269
5.4
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Ruegeria pomeroyi
2.1.1.269
5.4
-
dimethylsulfoniopropionate
-
Ruegeria pomeroyi
2.1.1.269
8.6
-
dimethylsulfoniopropionate
in cell extracts, similar to that of purified recombinant DmdA
Ruegeria pomeroyi
2.1.1.269
13.2
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Candidatus Pelagibacter ubique
2.1.1.269
13.2
-
dimethylsulfoniopropionate
-
Candidatus Pelagibacter ubique
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
2.1.1.269
38500
-
SDS-PAGE
Candidatus Pelagibacter ubique
2.1.1.269
38500
-
2 * 38500, SDS-PAGE
Candidatus Pelagibacter ubique
2.1.1.269
38500
-
2 * 38500, SDS-PAGE
Ruegeria pomeroyi
2.1.1.269
68000
-
PAGE
Candidatus Pelagibacter ubique
2.1.1.269
68000
-
PAGE
Ruegeria pomeroyi
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
2.1.1.269
anion-exchange, hydrophobic interaction, and hydroxyapatite chromatographies
Candidatus Pelagibacter ubique
2.1.1.269
anion-exchange, hydrophobic interaction, and hydroxyapatite chromatographies; recombinant protein
Ruegeria pomeroyi
2.1.1.269
recombinant protein
Candidatus Pelagibacter ubique
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2.1.1.269
2-(dimethylsulfonio)propanoate + tetrahydrofolate
enzyme exhibits strict substrate specificity for 2-(dimethylsulfonio)propanoate
698600
Candidatus Pelagibacter ubique
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
2-(dimethylsulfonio)propanoate + tetrahydrofolate
enzyme exhibits strict substrate specificity for 2-(dimethylsulfonio)propanoate
698600
Ruegeria pomeroyi
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
2-(dimethylsulfonio)propanoate + tetrahydrofolate
enzyme exhibits strict substrate specificity for 2-(dimethylsulfonio)propanoate
698600
Candidatus Pelagibacter ubique HTCC1062
2-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
3-(S,S-dimethylsulfonio)propanoate + tetrahydrofolate
-
698600
Candidatus Pelagibacter ubique
3-(methylthio)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
3-(S,S-dimethylsulfonio)propanoate + tetrahydrofolate
-
698600
Ruegeria pomeroyi
3-(methylthio)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
3-(S,S-dimethylsulfonio)propanoate + tetrahydrofolate
-
698600
Candidatus Pelagibacter ubique HTCC1062
3-(methylthio)propanoate + 5-methyltetrahydrofolate
-
-
-
?
2.1.1.269
additional information
no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity is found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Candidatus Pelagibacter ubique
?
-
-
-
-
2.1.1.269
additional information
no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity is found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Ruegeria pomeroyi
?
-
-
-
-
2.1.1.269
additional information
strict substrate specificity for dimethylsulfoniopropionate. No detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate and less than 1% activity with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Ruegeria pomeroyi
?
-
-
-
-
2.1.1.269
additional information
strict substrate specificity for dimethylsulfoniopropionate. No detectable demethylase activity with glycine betaine,dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate and less than 1% activity with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Candidatus Pelagibacter ubique
?
-
-
-
-
2.1.1.269
additional information
no detectable demethylase activity with glycine betaine, dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate. Less than 1% activity is found with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Candidatus Pelagibacter ubique HTCC1062
?
-
-
-
-
2.1.1.269
additional information
strict substrate specificity for dimethylsulfoniopropionate. No detectable demethylase activity with glycine betaine,dimethyl glycine, methylmercaptopropionate, methionine, or dimethylsulfonioacetate and less than 1% activity with dimethylsulfoniobutanoate and dimethylsulfoniopentanoate
698600
Candidatus Pelagibacter ubique HTCC1062
?
-
-
-
-
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
2.1.1.269
dimer
under nondenaturing conditions, MW is 68000 Da, suggesting that the enzyme is likely to be a dimer
Candidatus Pelagibacter ubique
2.1.1.269
dimer
2 * 38500, SDS-PAGE
Candidatus Pelagibacter ubique
2.1.1.269
dimer
2 * 38500, SDS-PAGE
Ruegeria pomeroyi
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
2.1.1.269
2.4
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Ruegeria pomeroyi
2.1.1.269
2.4
-
dimethylsulfoniopropionate
-
Ruegeria pomeroyi
2.1.1.269
8.1
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Candidatus Pelagibacter ubique
2.1.1.269
8.1
-
dimethylsulfoniopropionate
-
Candidatus Pelagibacter ubique
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
2.1.1.269
7
8
maximum activity is observed at pH 7.0 to 8.0
Candidatus Pelagibacter ubique
2.1.1.269
7
8
enzyme is more active in HEPES buffer than in MOPS or Tris-HCl buffer at the same pH
Candidatus Pelagibacter ubique
2.1.1.269
7
8
enzyme is more active in HEPES than in MOPS buffer, but the activities in HEPES and Tris-HCl buffers are the same; maximum activity is observed at pH 7.0 to 8.0
Ruegeria pomeroyi
pH Range (protein specific)
EC Number
pH Minimum
pH Maximum
Commentary
Organism
2.1.1.269
6
8.8
maximum activity is observed at pH 7.0 to 8.0, about 50% activity at pH 6.0 and 8.8; more than 50% of maximum activity within
Ruegeria pomeroyi
2.1.1.269
6.5
8.3
maximum activity is observed at pH 7.0 to 8.0, about 50% activity at pH 6.5 and 8.3
Candidatus Pelagibacter ubique
2.1.1.269
6.5
8.3
more than 50% of maximum activity within
Candidatus Pelagibacter ubique
KCat/KM [mM/s]
EC Number
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
2.1.1.269
0.45
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Ruegeria pomeroyi
2.1.1.269
0.618
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Candidatus Pelagibacter ubique
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
2.1.1.269
0.45
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Ruegeria pomeroyi
2.1.1.269
0.618
-
3-(S,S-dimethylsulfonio)propanoate
pH 7.5, temperature not specified in the publication
Candidatus Pelagibacter ubique