BRENDA - Enzyme Database

Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity

Xu, X.; Zhao, J.; Xu, Z.; Peng, B.; Huang, Q.; Arnold, E.; Ding, J.; J. Biol. Chem. 279, 33946-33957 (2004)

Data extracted from this reference:

Activating Compound
EC Number
Activating Compound
Commentary
Organism
Structure
1.1.1.42
additional information
glucose induces epression of isozyme IDP1, glycerol induces epression of isozymes IDP1 and IDP2, fatty acids induce epression of isozymes IDP1, IDP2, and IDP3
Saccharomyces cerevisiae
Cloned(Commentary)
EC Number
Commentary
Organism
1.1.1.42
expression of C-terminally His-tagged enzyme in Escherichia coli BL21(DE3)
Homo sapiens
1.1.1.42
expression of isozyme IDP1 and IDP2 as His-tagged enzymes in a disruption mutant
Saccharomyces cerevisiae
Crystallization (Commentary)
EC Number
Crystallization
Organism
1.1.1.42
hanging drop vapour diffusion method, purified recombinant His-tagged enzyme in complex with NADP+: equal volume of protein solution, containing 15 mg/ml enzyme, 20 mM Tris-HCl, pH 7.4, 100 mM NaCl, and 10 mM NADP+, and of reservoir solution, containing 100 mM MES, pH 6.5, 12% PEG 20000, at 4C, purified recombinant His-tagged enzyme in complex with NADP+, isocitrate and Ca2+: equal volume of protein solution, containing 15 mg/ml enzyme, 20 mM Tris-HCl, pH 7.4, 100 mM NaCl, and 10 mM NADP+, 10 mM DL-isocitrate and 10 mM CaCl2, and of reservoir solution, containing 100 mM MES, pH 5.9, 20% PEG 6000, at 20C, X-ray diffraction structure determination and analysis
Homo sapiens
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
1.1.1.42
additional information
-
additional information
kinetics of isozymes IDP1 and IDP2
Saccharomyces cerevisiae
Localization
EC Number
Localization
Commentary
Organism
GeneOntology No.
Textmining
1.1.1.42
cytosol
isozyme IDP2
Saccharomyces cerevisiae
5829
-
1.1.1.42
cytosol
-
Homo sapiens
5829
-
1.1.1.42
mitochondrion
isozyme IDP1
Saccharomyces cerevisiae
5739
-
1.1.1.42
peroxisome
isoyzme IDP3
Saccharomyces cerevisiae
5777
-
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.42
Ca2+
divalent metal ion is required, binding structure and conformation at the isocitrate-metal-binding site
Homo sapiens
1.1.1.42
Mg2+
divalent metal ion is required, binding structure and conformation at the isocitrate-metal-binding site
Homo sapiens
1.1.1.42
Mg2+
-
Saccharomyces cerevisiae
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.1.1.42
46381
-
x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry
Saccharomyces cerevisiae
1.1.1.42
46562
-
x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry
Saccharomyces cerevisiae
1.1.1.42
47856
-
x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry
Saccharomyces cerevisiae
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
D-isocitrate + NADP+
Saccharomyces cerevisiae
the reaction is reversible for isozyme IDP2
2-oxoglutarate + CO2 + NADPH
-
-
r
1.1.1.42
isocitrate + NADP+
Homo sapiens
enzyme has a self-regulatory mechanism of activity mimicking the phosphorylation mechanism of bacterial enzymes
2-oxoglutarate + CO2 + NADPH
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.1.1.42
Homo sapiens
-
-
-
1.1.1.42
Saccharomyces cerevisiae
-
1 cytosolic, 1 peroxisomal, and 1 mitochondrial isozyme
-
Purification (Commentary)
EC Number
Commentary
Organism
1.1.1.42
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography
Homo sapiens
1.1.1.42
recombinant His-tagged isozymes IDP1 and IDP2 by nickel affinity chromatography
Saccharomyces cerevisiae
Reaction
EC Number
Reaction
Commentary
Organism
1.1.1.42
isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+
active site structure and reaction mechanism, conformational changes at the active site resulting in closed and open forms, regulatory residues are isocitrate-binding Asp279and Ser94
Homo sapiens
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.1.1.42
D-isocitrate + NADP+
the reaction is reversible for isozyme IDP2
656233
Saccharomyces cerevisiae
2-oxoglutarate + CO2 + NADPH
-
-
-
r
1.1.1.42
isocitrate + NADP+
-
656233
Homo sapiens
2-oxoglutarate + CO2 + NADPH
-
-
-
?
1.1.1.42
isocitrate + NADP+
enzyme has a self-regulatory mechanism of activity mimicking the phosphorylation mechanism of bacterial enzymes
656233
Homo sapiens
2-oxoglutarate + CO2 + NADPH
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
1.1.1.42
?
x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry
Saccharomyces cerevisiae
1.1.1.42
More
enzyme has 3 different conformational stages
Homo sapiens
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.42
6.5
-
assay at, reverse reaction
Saccharomyces cerevisiae
1.1.1.42
7.4
-
assay at
Homo sapiens
1.1.1.42
7.5
-
isozyme IDP2, forward reaction
Saccharomyces cerevisiae
1.1.1.42
8
-
isozyme IDP1, forward reaction
Saccharomyces cerevisiae
pH Range
EC Number
pH Minimum
pH Maximum
Commentary
Organism
1.1.1.42
6
9.5
-
Saccharomyces cerevisiae
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.42
NADP+
binding site structure, interaction with the 2'-phosphate group of the ribose moiety
Homo sapiens
1.1.1.42
NADP+
-
Saccharomyces cerevisiae
1.1.1.42
NADPH
-
Saccharomyces cerevisiae
pI Value
EC Number
Organism
Commentary
pI Value Maximum
pI Value
1.1.1.42
Saccharomyces cerevisiae
isozyme IDP2
-
5.5
1.1.1.42
Saccharomyces cerevisiae
isozyme IDP1
-
8.5
1.1.1.42
Saccharomyces cerevisiae
isozyme IDP3
-
10
Activating Compound (protein specific)
EC Number
Activating Compound
Commentary
Organism
Structure
1.1.1.42
additional information
glucose induces epression of isozyme IDP1, glycerol induces epression of isozymes IDP1 and IDP2, fatty acids induce epression of isozymes IDP1, IDP2, and IDP3
Saccharomyces cerevisiae
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.42
expression of C-terminally His-tagged enzyme in Escherichia coli BL21(DE3)
Homo sapiens
1.1.1.42
expression of isozyme IDP1 and IDP2 as His-tagged enzymes in a disruption mutant
Saccharomyces cerevisiae
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.1.1.42
NADP+
binding site structure, interaction with the 2'-phosphate group of the ribose moiety
Homo sapiens
1.1.1.42
NADP+
-
Saccharomyces cerevisiae
1.1.1.42
NADPH
-
Saccharomyces cerevisiae
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
1.1.1.42
hanging drop vapour diffusion method, purified recombinant His-tagged enzyme in complex with NADP+: equal volume of protein solution, containing 15 mg/ml enzyme, 20 mM Tris-HCl, pH 7.4, 100 mM NaCl, and 10 mM NADP+, and of reservoir solution, containing 100 mM MES, pH 6.5, 12% PEG 20000, at 4C, purified recombinant His-tagged enzyme in complex with NADP+, isocitrate and Ca2+: equal volume of protein solution, containing 15 mg/ml enzyme, 20 mM Tris-HCl, pH 7.4, 100 mM NaCl, and 10 mM NADP+, 10 mM DL-isocitrate and 10 mM CaCl2, and of reservoir solution, containing 100 mM MES, pH 5.9, 20% PEG 6000, at 20C, X-ray diffraction structure determination and analysis
Homo sapiens
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
kinetics of isozymes IDP1 and IDP2
Saccharomyces cerevisiae
Localization (protein specific)
EC Number
Localization
Commentary
Organism
GeneOntology No.
Textmining
1.1.1.42
cytosol
isozyme IDP2
Saccharomyces cerevisiae
5829
-
1.1.1.42
cytosol
-
Homo sapiens
5829
-
1.1.1.42
mitochondrion
isozyme IDP1
Saccharomyces cerevisiae
5739
-
1.1.1.42
peroxisome
isoyzme IDP3
Saccharomyces cerevisiae
5777
-
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
1.1.1.42
Ca2+
divalent metal ion is required, binding structure and conformation at the isocitrate-metal-binding site
Homo sapiens
1.1.1.42
Mg2+
divalent metal ion is required, binding structure and conformation at the isocitrate-metal-binding site
Homo sapiens
1.1.1.42
Mg2+
-
Saccharomyces cerevisiae
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.1.1.42
46381
-
x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry
Saccharomyces cerevisiae
1.1.1.42
46562
-
x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry
Saccharomyces cerevisiae
1.1.1.42
47856
-
x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry
Saccharomyces cerevisiae
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
D-isocitrate + NADP+
Saccharomyces cerevisiae
the reaction is reversible for isozyme IDP2
2-oxoglutarate + CO2 + NADPH
-
-
r
1.1.1.42
isocitrate + NADP+
Homo sapiens
enzyme has a self-regulatory mechanism of activity mimicking the phosphorylation mechanism of bacterial enzymes
2-oxoglutarate + CO2 + NADPH
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
1.1.1.42
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography
Homo sapiens
1.1.1.42
recombinant His-tagged isozymes IDP1 and IDP2 by nickel affinity chromatography
Saccharomyces cerevisiae
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
D-isocitrate + NADP+
the reaction is reversible for isozyme IDP2
656233
Saccharomyces cerevisiae
2-oxoglutarate + CO2 + NADPH
-
-
-
r
1.1.1.42
isocitrate + NADP+
-
656233
Homo sapiens
2-oxoglutarate + CO2 + NADPH
-
-
-
?
1.1.1.42
isocitrate + NADP+
enzyme has a self-regulatory mechanism of activity mimicking the phosphorylation mechanism of bacterial enzymes
656233
Homo sapiens
2-oxoglutarate + CO2 + NADPH
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.1.1.42
?
x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry
Saccharomyces cerevisiae
1.1.1.42
More
enzyme has 3 different conformational stages
Homo sapiens
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
1.1.1.42
6.5
-
assay at, reverse reaction
Saccharomyces cerevisiae
1.1.1.42
7.4
-
assay at
Homo sapiens
1.1.1.42
7.5
-
isozyme IDP2, forward reaction
Saccharomyces cerevisiae
1.1.1.42
8
-
isozyme IDP1, forward reaction
Saccharomyces cerevisiae
pH Range (protein specific)
EC Number
pH Minimum
pH Maximum
Commentary
Organism
1.1.1.42
6
9.5
-
Saccharomyces cerevisiae
pI Value (protein specific)
EC Number
Organism
Commentary
pI Value Maximum
pI Value
1.1.1.42
Saccharomyces cerevisiae
isozyme IDP2
-
5.5
1.1.1.42
Saccharomyces cerevisiae
isozyme IDP1
-
8.5
1.1.1.42
Saccharomyces cerevisiae
isozyme IDP3
-
10