BRENDA - Enzyme Database

A novel type II NAD+-specific isocitrate dehydrogenase from the marine bacterium Congregibacter litoralis KT71

Wu, M.; Tian, C.; Cheng, H.; Xu, L.; Wang, P.; Zhu, G.; PLoS ONE 10, e0125229 (2015)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
1.1.1.41
gene KT71_12905, DNA and amino acid sequence determination and analysis, sequence comparisons,, phylogenetic analysis and tree, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain Rosetta (DE3)
Congregibacter litoralis
Engineering
EC Number
Amino acid exchange
Commentary
Organism
1.1.1.41
D487R/L488H
site-directed mutagenesis, the coenzyme specificity of a the ClIDH mutant is altered compared to the wild-type enzyme, and the preference of the mutant for NADP+ is approximately 24fold higher than that for NAD+, suggesting that ClIDH is an NAD+-specific ancestral enzyme in the type II IDH subgroup
Congregibacter litoralis
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.41
0.157
-
NADP+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
0.263
-
NAD+
wild-type enzyme, with Mg2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
0.309
-
NAD+
wild-type enzyme, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
0.664
-
NAD+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.41
Co2+
activates, 38.3% activity compared to Mn2+
Congregibacter litoralis
1.1.1.41
Mg2+
activates, 45.7% activity compared to Mn2+
Congregibacter litoralis
1.1.1.41
Mn2+
most effectivly activating cation
Congregibacter litoralis
1.1.1.41
additional information
enzyme ClIDH is dependent on divalent cations, the most effective being Mn2+. Poor activation by Ca2+, Zn2+, Ni2+, K+, Na+, Rb+, and Li+. No activation by Cu2+
Congregibacter litoralis
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.1.1.41
64000
-
-
Congregibacter litoralis
1.1.1.41
390000
-
recombinant His6-tagged enzyme, gel filtration and analytical ultracentrifugation
Congregibacter litoralis
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
isocitrate + NAD+
Congregibacter litoralis
-
2-oxoglutarate + CO2 + NADH
-
-
?
1.1.1.41
isocitrate + NAD+
Congregibacter litoralis KT71
-
2-oxoglutarate + CO2 + NADH
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.41
Congregibacter litoralis
A4ADB8
-
-
1.1.1.41
Congregibacter litoralis KT71
A4ADB8
-
-
Purification (Commentary)
EC Number
Commentary
Organism
1.1.1.41
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain Rosetta (DE3) by metal affinity chromatography
Congregibacter litoralis
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.41
isocitrate + NAD+
-
741236
Congregibacter litoralis
2-oxoglutarate + CO2 + NADH
-
-
-
?
1.1.1.41
isocitrate + NAD+
-
741236
Congregibacter litoralis KT71
2-oxoglutarate + CO2 + NADH
-
-
-
?
1.1.1.41
isocitrate + NADP+
activity with enzyme mutant D487R/L488H, not the wild-type enzyme
741236
Congregibacter litoralis
2-oxoglutarate + CO2 + NADPH
-
-
-
?
1.1.1.41
isocitrate + NADP+
activity with enzyme mutant D487R/L488H, not the wild-type enzyme
741236
Congregibacter litoralis KT71
2-oxoglutarate + CO2 + NADPH
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
1.1.1.41
homohexamer
6 * 64000, recombinant His6-tagged enzyme, SDS-PAGE
Congregibacter litoralis
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.41
35
-
-
Congregibacter litoralis
Temperature Range [°C]
EC Number
Temperature Minimum [°C]
Temperature Maximum [°C]
Commentary
Organism
1.1.1.41
20
32
activity range, profile overview
Congregibacter litoralis
Temperature Stability [°C]
EC Number
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
1.1.1.41
33
-
purified recombinant enzyme, 20 min, loss of 50% activity
Congregibacter litoralis
1.1.1.41
38
-
purified recombinant enzyme, 20 min, loss of over 90% activity
Congregibacter litoralis
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
1.1.1.41
9.7
-
NAD+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
36.7
-
NAD+
wild-type enzyme, with Mg2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
55.1
-
NADP+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
84.7
-
NAD+
wild-type enzyme, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.41
7.5
-
-
Congregibacter litoralis
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.41
NAD+
the recombinant enzyme is NAD+-specific and shows no detectable activity with NADP+
Congregibacter litoralis
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.41
gene KT71_12905, DNA and amino acid sequence determination and analysis, sequence comparisons,, phylogenetic analysis and tree, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain Rosetta (DE3)
Congregibacter litoralis
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.41
NAD+
the recombinant enzyme is NAD+-specific and shows no detectable activity with NADP+
Congregibacter litoralis
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
1.1.1.41
D487R/L488H
site-directed mutagenesis, the coenzyme specificity of a the ClIDH mutant is altered compared to the wild-type enzyme, and the preference of the mutant for NADP+ is approximately 24fold higher than that for NAD+, suggesting that ClIDH is an NAD+-specific ancestral enzyme in the type II IDH subgroup
Congregibacter litoralis
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.41
0.157
-
NADP+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
0.263
-
NAD+
wild-type enzyme, with Mg2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
0.309
-
NAD+
wild-type enzyme, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
0.664
-
NAD+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.41
Co2+
activates, 38.3% activity compared to Mn2+
Congregibacter litoralis
1.1.1.41
Mg2+
activates, 45.7% activity compared to Mn2+
Congregibacter litoralis
1.1.1.41
Mn2+
most effectivly activating cation
Congregibacter litoralis
1.1.1.41
additional information
enzyme ClIDH is dependent on divalent cations, the most effective being Mn2+. Poor activation by Ca2+, Zn2+, Ni2+, K+, Na+, Rb+, and Li+. No activation by Cu2+
Congregibacter litoralis
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.1.1.41
64000
-
-
Congregibacter litoralis
1.1.1.41
390000
-
recombinant His6-tagged enzyme, gel filtration and analytical ultracentrifugation
Congregibacter litoralis
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
isocitrate + NAD+
Congregibacter litoralis
-
2-oxoglutarate + CO2 + NADH
-
-
?
1.1.1.41
isocitrate + NAD+
Congregibacter litoralis KT71
-
2-oxoglutarate + CO2 + NADH
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.41
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain Rosetta (DE3) by metal affinity chromatography
Congregibacter litoralis
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
isocitrate + NAD+
-
741236
Congregibacter litoralis
2-oxoglutarate + CO2 + NADH
-
-
-
?
1.1.1.41
isocitrate + NAD+
-
741236
Congregibacter litoralis KT71
2-oxoglutarate + CO2 + NADH
-
-
-
?
1.1.1.41
isocitrate + NADP+
activity with enzyme mutant D487R/L488H, not the wild-type enzyme
741236
Congregibacter litoralis
2-oxoglutarate + CO2 + NADPH
-
-
-
?
1.1.1.41
isocitrate + NADP+
activity with enzyme mutant D487R/L488H, not the wild-type enzyme
741236
Congregibacter litoralis KT71
2-oxoglutarate + CO2 + NADPH
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.1.1.41
homohexamer
6 * 64000, recombinant His6-tagged enzyme, SDS-PAGE
Congregibacter litoralis
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
1.1.1.41
35
-
-
Congregibacter litoralis
Temperature Range [°C] (protein specific)
EC Number
Temperature Minimum [°C]
Temperature Maximum [°C]
Commentary
Organism
1.1.1.41
20
32
activity range, profile overview
Congregibacter litoralis
Temperature Stability [°C] (protein specific)
EC Number
Temperature Stability Minimum [°C]
Temperature Stability Maximum [°C]
Commentary
Organism
1.1.1.41
33
-
purified recombinant enzyme, 20 min, loss of 50% activity
Congregibacter litoralis
1.1.1.41
38
-
purified recombinant enzyme, 20 min, loss of over 90% activity
Congregibacter litoralis
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
9.7
-
NAD+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
36.7
-
NAD+
wild-type enzyme, with Mg2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
55.1
-
NADP+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
84.7
-
NAD+
wild-type enzyme, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.41
7.5
-
-
Congregibacter litoralis
General Information
EC Number
General Information
Commentary
Organism
1.1.1.41
evolution
phylogenetic analyses divide the IDH protein family into two subgroups: types I and II. Based on cofactor usage, IDHs are either NAD+-specific (NAD-IDH) or NADP+-specific (NADP-IDH). NADP-IDH evolved from NAD-IDH. Type I IDHs include NAD-IDHs and NADP-IDHs. Type II NAD-IDHs is identified from the marine bacterium Congregibacter litoralis KT71, i.e ClIDH. Evolutionary relationships between 151 IDHs from different organisms, overview
Congregibacter litoralis
General Information (protein specific)
EC Number
General Information
Commentary
Organism
1.1.1.41
evolution
phylogenetic analyses divide the IDH protein family into two subgroups: types I and II. Based on cofactor usage, IDHs are either NAD+-specific (NAD-IDH) or NADP+-specific (NADP-IDH). NADP-IDH evolved from NAD-IDH. Type I IDHs include NAD-IDHs and NADP-IDHs. Type II NAD-IDHs is identified from the marine bacterium Congregibacter litoralis KT71, i.e ClIDH. Evolutionary relationships between 151 IDHs from different organisms, overview
Congregibacter litoralis
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
15
-
NAD+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
140
-
NAD+
wild-type enzyme, with Mg2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
270
-
NAD+
wild-type enzyme, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
350
-
NADP+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
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
15
-
NAD+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
140
-
NAD+
wild-type enzyme, with Mg2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
270
-
NAD+
wild-type enzyme, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis
1.1.1.41
350
-
NADP+
mutant D487R/L488H, with Mn2+, pH 7.5, 35°C
Congregibacter litoralis