BRENDA - Enzyme Database

Structural, kinetic and chemical mechanism of isocitrate dehydrogenase-1 from Mycobacterium tuberculosis

Quartararo, C.E.; Hazra, S.; Hadi, T.; Blanchard, J.S.; Biochemistry 52, 1765-1775 (2013)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
1.1.1.42
gene Rv3339c, expression of N-terminally His6-tagged enzyme
Mycobacterium tuberculosis
Crystallization (Commentary)
EC Number
Crystallization
Organism
1.1.1.42
purified ICDH-1 in complex with NADPH at Mn2+, hanging drop vapor diffusion method, 0.001 ml of protein in 5 mM NADPH, and 5 mM MnCl2 is mixed with 0.001 ml of reservoir solution containing 30% PEG 2000 and 0.1 M Tris-HCl, pH 8.0, room temperature, X-ray diffraction structure determination and analysis at 2.18 A resoltuion
Mycobacterium tuberculosis
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.42
2-oxoglutarate
noncompetitive versus NADP+
Mycobacterium tuberculosis
1.1.1.42
malate
noncompetitive versus NADP+ and isocitrate
Mycobacterium tuberculosis
1.1.1.42
additional information
product inhibition patterns for ICDH-1, overview
Mycobacterium tuberculosis
1.1.1.42
NADPH
product inhibition competitive versus NADP+ and noncompetitive versus isocitrate
Mycobacterium tuberculosis
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.42
additional information
-
additional information
steady-state kinetics, kinetic mechanism of ICDH-1, overview
Mycobacterium tuberculosis
1.1.1.42
0.015
-
NADP+
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
Mycobacterium tuberculosis
1.1.1.42
0.05
-
isocitrate
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
Mycobacterium tuberculosis
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.42
Mn2+
required
Mycobacterium tuberculosis
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.42
isocitrate + NADP+
Mycobacterium tuberculosis
-
2-oxoglutarate + CO2 + NADPH + H+
-
-
?
1.1.1.42
isocitrate + NADP+
Mycobacterium tuberculosis H37Rv
-
2-oxoglutarate + CO2 + NADPH + H+
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.42
Mycobacterium tuberculosis
P9WKL1
gene Rv3339c
-
1.1.1.42
Mycobacterium tuberculosis H37Rv
P9WKL1
gene Rv3339c
-
Purification (Commentary)
EC Number
Commentary
Organism
1.1.1.42
recombinant N-terminally His6-tagged enzyme by nickel affinity chromatography and gel filtration
Mycobacterium tuberculosis
Reaction
EC Number
Reaction
Commentary
Organism
1.1.1.42
isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+
protonation of the enolate to form product 2-oxoglutarate is the rate-limiting step
Mycobacterium tuberculosis
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.42
isocitrate + NADP+
-
721687
Mycobacterium tuberculosis
2-oxoglutarate + CO2 + NADPH + H+
-
-
-
?
1.1.1.42
isocitrate + NADP+
-
721687
Mycobacterium tuberculosis H37Rv
2-oxoglutarate + CO2 + NADPH + H+
-
-
-
?
1.1.1.42
additional information
Mycobacterium tuberculosis ICDH-1 also catalyzes the formation of 2-hydroxyglutarate
721687
Mycobacterium tuberculosis
?
-
-
-
-
1.1.1.42
additional information
Mycobacterium tuberculosis ICDH-1 also catalyzes the formation of 2-hydroxyglutarate
721687
Mycobacterium tuberculosis H37Rv
?
-
-
-
-
Subunits
EC Number
Subunits
Commentary
Organism
1.1.1.42
homodimer
each subunit has a Rossmann fold, and a common top domain of interlocking beta sheets
Mycobacterium tuberculosis
1.1.1.42
More
three-dimensional structure of Mtb ICDH-1, overview
Mycobacterium tuberculosis
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
1.1.1.42
33
-
isocitrate
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
Mycobacterium tuberculosis
1.1.1.42
33
-
NADP+
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
Mycobacterium tuberculosis
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.42
7.5
-
assay at
Mycobacterium tuberculosis
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.42
NADP+
-
Mycobacterium tuberculosis
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.42
gene Rv3339c, expression of N-terminally His6-tagged enzyme
Mycobacterium tuberculosis
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.42
NADP+
-
Mycobacterium tuberculosis
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
1.1.1.42
purified ICDH-1 in complex with NADPH at Mn2+, hanging drop vapor diffusion method, 0.001 ml of protein in 5 mM NADPH, and 5 mM MnCl2 is mixed with 0.001 ml of reservoir solution containing 30% PEG 2000 and 0.1 M Tris-HCl, pH 8.0, room temperature, X-ray diffraction structure determination and analysis at 2.18 A resoltuion
Mycobacterium tuberculosis
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
1.1.1.42
2-oxoglutarate
noncompetitive versus NADP+
Mycobacterium tuberculosis
1.1.1.42
malate
noncompetitive versus NADP+ and isocitrate
Mycobacterium tuberculosis
1.1.1.42
additional information
product inhibition patterns for ICDH-1, overview
Mycobacterium tuberculosis
1.1.1.42
NADPH
product inhibition competitive versus NADP+ and noncompetitive versus isocitrate
Mycobacterium tuberculosis
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.42
additional information
-
additional information
steady-state kinetics, kinetic mechanism of ICDH-1, overview
Mycobacterium tuberculosis
1.1.1.42
0.015
-
NADP+
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
Mycobacterium tuberculosis
1.1.1.42
0.05
-
isocitrate
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
Mycobacterium tuberculosis
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.42
Mn2+
required
Mycobacterium tuberculosis
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.1.1.42
isocitrate + NADP+
Mycobacterium tuberculosis
-
2-oxoglutarate + CO2 + NADPH + H+
-
-
?
1.1.1.42
isocitrate + NADP+
Mycobacterium tuberculosis H37Rv
-
2-oxoglutarate + CO2 + NADPH + H+
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.42
recombinant N-terminally His6-tagged enzyme by nickel affinity chromatography and gel filtration
Mycobacterium tuberculosis
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.42
isocitrate + NADP+
-
721687
Mycobacterium tuberculosis
2-oxoglutarate + CO2 + NADPH + H+
-
-
-
?
1.1.1.42
isocitrate + NADP+
-
721687
Mycobacterium tuberculosis H37Rv
2-oxoglutarate + CO2 + NADPH + H+
-
-
-
?
1.1.1.42
additional information
Mycobacterium tuberculosis ICDH-1 also catalyzes the formation of 2-hydroxyglutarate
721687
Mycobacterium tuberculosis
?
-
-
-
-
1.1.1.42
additional information
Mycobacterium tuberculosis ICDH-1 also catalyzes the formation of 2-hydroxyglutarate
721687
Mycobacterium tuberculosis H37Rv
?
-
-
-
-
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.1.1.42
homodimer
each subunit has a Rossmann fold, and a common top domain of interlocking beta sheets
Mycobacterium tuberculosis
1.1.1.42
More
three-dimensional structure of Mtb ICDH-1, overview
Mycobacterium tuberculosis
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
1.1.1.42
33
-
isocitrate
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
Mycobacterium tuberculosis
1.1.1.42
33
-
NADP+
pH 7.5, temperature not specified in the publication, recombinant His-tagged enzyme
Mycobacterium tuberculosis
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.42
7.5
-
assay at
Mycobacterium tuberculosis