BRENDA - Enzyme Database

Isocitrate dehydrogenase from Streptococcus mutans: biochemical properties and evaluation of a putative phosphorylation site at Ser102

Wang, P.; Song, P.; Jin, M.; Zhu, G.; PLoS ONE 8, e58918 (2013)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
1.1.1.41
gene idh, expression of wild-type and mutant enzymes in Escherichia coli glutamate auxotrophic strain Dicd::kanr fused to gene icd, the endogenous icd gene is replaced by the kanamycin resistance gene, the wild-type phenotype of the icd defective strain on minimal medium without glutamate is restored
Streptococcus mutans
Engineering
EC Number
Amino acid exchange
Commentary
Organism
1.1.1.41
S102A
site-directed mutagenesis, the mutant shows decreased affinity for isocitrate and 3.3% of wild-type activity
Streptococcus mutans
1.1.1.41
S102G
site-directed mutagenesis, the mutant shows decreased affinity for isocitrate and 2.8% of wild-type activity
Streptococcus mutans
1.1.1.41
S102T
site-directed mutagenesis, the mutant shows decreased affinity for isocitrate and 16% of wild-type activity
Streptococcus mutans
1.1.1.41
S102Y
site-directed mutagenesis, the mutant shows decreased affinity for isocitrate and 1.1% of wild-type activity
Streptococcus mutans
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.41
Ca2+
-
Streptococcus mutans
1.1.1.41
Co2+
-
Streptococcus mutans
1.1.1.41
Cu2+
-
Streptococcus mutans
1.1.1.41
Ni2+
-
Streptococcus mutans
1.1.1.41
Zn2+
-
Streptococcus mutans
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.41
0.075
-
DL-isocitrate
pH 7.5, 37°C, recombinant wild-type enzyme
Streptococcus mutans
1.1.1.41
0.143
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
0.148
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
0.15
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
0.154
-
NAD+
pH 7.5, 37°C, recombinant enzyme
Streptococcus mutans
1.1.1.41
0.246
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
0.295
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
0.35
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
0.385
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
1.1.1.41
1.56
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.41
Mn2+
best divalent cation
Streptococcus mutans
1.1.1.41
additional information
the enzyme is dependent on divalent cations
Streptococcus mutans
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.1.1.41
70000
-
recombinant enzyme, gel filtration
Streptococcus mutans
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.41
DL-isocitrate + NAD+
Streptococcus mutans
-
2-oxoglutarate + CO2 + NADH
-
-
r
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.41
Streptococcus mutans
-
-
-
Posttranslational Modification
EC Number
Posttranslational Modification
Commentary
Organism
1.1.1.41
phosphoprotein
catalytically important phosphorylation site at Ser102
Streptococcus mutans
Purification (Commentary)
EC Number
Commentary
Organism
1.1.1.41
recombinant wild-type and mutant enzymes from Escherichia coli
Streptococcus mutans
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.41
DL-isocitrate + NAD+
-
723607
Streptococcus mutans
2-oxoglutarate + CO2 + NADH
-
-
-
r
1.1.1.41
additional information
the enzyme is also active with NADP+ and NADPH, cf. EC 1.1.1.42
723607
Streptococcus mutans
?
-
-
-
-
Subunits
EC Number
Subunits
Commentary
Organism
1.1.1.41
homodimer
-
Streptococcus mutans
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.41
45
-
-
Streptococcus mutans
Temperature Range [°C]
EC Number
Temperature Minimum [°C]
Temperature Maximum [°C]
Commentary
Organism
1.1.1.41
25
55
activity range, profile overview
Streptococcus mutans
Temperature Stability [°C]
EC Number
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
1.1.1.41
40
-
purified recombinant enzyme, stable up to, rapid inactivation above
Streptococcus mutans
1.1.1.41
50
-
purified recombinant enzyme, inactivation
Streptococcus mutans
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
1.1.1.41
1.5
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
1.1.1.41
3
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
3.3
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
3.5
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
1.1.1.41
4
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
9.1
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
25
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
56
-
NAD+
pH 7.5, 37°C, recombinant wild-type enzyme
Streptococcus mutans
1.1.1.41
59
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
124
-
DL-isocitrate
pH 7.5, 37°C, recombinant wild-type enzyme
Streptococcus mutans
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.41
7.8
-
-
Streptococcus mutans
pH Range
EC Number
pH Minimum
pH Maximum
Commentary
Organism
1.1.1.41
7.2
9.2
activity range, profile overview
Streptococcus mutans
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.41
additional information
the enzyme is also active with NADP+ and NADPH, cf. EC 1.1.1.42
Streptococcus mutans
1.1.1.41
NAD+
-
Streptococcus mutans
1.1.1.41
NADH
-
Streptococcus mutans
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.41
gene idh, expression of wild-type and mutant enzymes in Escherichia coli glutamate auxotrophic strain Dicd::kanr fused to gene icd, the endogenous icd gene is replaced by the kanamycin resistance gene, the wild-type phenotype of the icd defective strain on minimal medium without glutamate is restored
Streptococcus mutans
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.41
additional information
the enzyme is also active with NADP+ and NADPH, cf. EC 1.1.1.42
Streptococcus mutans
1.1.1.41
NAD+
-
Streptococcus mutans
1.1.1.41
NADH
-
Streptococcus mutans
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
1.1.1.41
S102A
site-directed mutagenesis, the mutant shows decreased affinity for isocitrate and 3.3% of wild-type activity
Streptococcus mutans
1.1.1.41
S102G
site-directed mutagenesis, the mutant shows decreased affinity for isocitrate and 2.8% of wild-type activity
Streptococcus mutans
1.1.1.41
S102T
site-directed mutagenesis, the mutant shows decreased affinity for isocitrate and 16% of wild-type activity
Streptococcus mutans
1.1.1.41
S102Y
site-directed mutagenesis, the mutant shows decreased affinity for isocitrate and 1.1% of wild-type activity
Streptococcus mutans
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.41
Ca2+
-
Streptococcus mutans
1.1.1.41
Co2+
-
Streptococcus mutans
1.1.1.41
Cu2+
-
Streptococcus mutans
1.1.1.41
Ni2+
-
Streptococcus mutans
1.1.1.41
Zn2+
-
Streptococcus mutans
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.41
0.075
-
DL-isocitrate
pH 7.5, 37°C, recombinant wild-type enzyme
Streptococcus mutans
1.1.1.41
0.143
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
0.148
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
0.15
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
0.154
-
NAD+
pH 7.5, 37°C, recombinant enzyme
Streptococcus mutans
1.1.1.41
0.246
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
0.295
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
0.35
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
0.385
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
1.1.1.41
1.56
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.41
Mn2+
best divalent cation
Streptococcus mutans
1.1.1.41
additional information
the enzyme is dependent on divalent cations
Streptococcus mutans
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.1.1.41
70000
-
recombinant enzyme, gel filtration
Streptococcus mutans
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.41
DL-isocitrate + NAD+
Streptococcus mutans
-
2-oxoglutarate + CO2 + NADH
-
-
r
Posttranslational Modification (protein specific)
EC Number
Posttranslational Modification
Commentary
Organism
1.1.1.41
phosphoprotein
catalytically important phosphorylation site at Ser102
Streptococcus mutans
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.41
recombinant wild-type and mutant enzymes from Escherichia coli
Streptococcus mutans
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.41
DL-isocitrate + NAD+
-
723607
Streptococcus mutans
2-oxoglutarate + CO2 + NADH
-
-
-
r
1.1.1.41
additional information
the enzyme is also active with NADP+ and NADPH, cf. EC 1.1.1.42
723607
Streptococcus mutans
?
-
-
-
-
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.1.1.41
homodimer
-
Streptococcus mutans
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.41
45
-
-
Streptococcus mutans
Temperature Range [°C] (protein specific)
EC Number
Temperature Minimum [°C]
Temperature Maximum [°C]
Commentary
Organism
1.1.1.41
25
55
activity range, profile overview
Streptococcus mutans
Temperature Stability [°C] (protein specific)
EC Number
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
1.1.1.41
40
-
purified recombinant enzyme, stable up to, rapid inactivation above
Streptococcus mutans
1.1.1.41
50
-
purified recombinant enzyme, inactivation
Streptococcus mutans
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
1.1.1.41
1.5
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
1.1.1.41
3
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
3.3
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
3.5
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
1.1.1.41
4
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
9.1
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
25
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
56
-
NAD+
pH 7.5, 37°C, recombinant wild-type enzyme
Streptococcus mutans
1.1.1.41
59
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
124
-
DL-isocitrate
pH 7.5, 37°C, recombinant wild-type enzyme
Streptococcus mutans
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.41
7.8
-
-
Streptococcus mutans
pH Range (protein specific)
EC Number
pH Minimum
pH Maximum
Commentary
Organism
1.1.1.41
7.2
9.2
activity range, profile overview
Streptococcus mutans
General Information
EC Number
General Information
Commentary
Organism
1.1.1.41
evolution
the ancient NAD-dependent IDHs might be the underlying origin of phosphorylation mechanism used by their bacterial NADP-dependent homologues
Streptococcus mutans
1.1.1.41
additional information
Ser102 plays an important role in substrate binding and is required for the enzyme function
Streptococcus mutans
General Information (protein specific)
EC Number
General Information
Commentary
Organism
1.1.1.41
evolution
the ancient NAD-dependent IDHs might be the underlying origin of phosphorylation mechanism used by their bacterial NADP-dependent homologues
Streptococcus mutans
1.1.1.41
additional information
Ser102 plays an important role in substrate binding and is required for the enzyme function
Streptococcus mutans
KCat/KM [mM/s]
EC Number
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
1.1.1.41
0.000002
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
1.1.1.41
0.000004
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
1.1.1.41
0.00001
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
0.000022
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
0.000028
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
0.00003
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
0.00017
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
0.00017
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
0.00036
-
NAD+
pH 7.5, 37°C, recombinant enzyme
Streptococcus mutans
1.1.1.41
0.00165
-
DL-isocitrate
pH 7.5, 37°C, recombinant wild-type enzyme
Streptococcus mutans
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
1.1.1.41
0.000002
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
1.1.1.41
0.000004
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102Y
Streptococcus mutans
1.1.1.41
0.00001
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
0.000022
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102A
Streptococcus mutans
1.1.1.41
0.000028
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
0.00003
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102G
Streptococcus mutans
1.1.1.41
0.00017
-
DL-isocitrate
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
0.00017
-
NAD+
pH 7.5, 37°C, recombinant enzyme mutant S102T
Streptococcus mutans
1.1.1.41
0.00036
-
NAD+
pH 7.5, 37°C, recombinant enzyme
Streptococcus mutans
1.1.1.41
0.00165
-
DL-isocitrate
pH 7.5, 37°C, recombinant wild-type enzyme
Streptococcus mutans