Literature summary for 1.1.1.42 extracted from

Xu, X.; Zhao, J.; Xu, Z.; Peng, B.; Huang, Q.; Arnold, E.; Ding, J.
Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity (2004), J. Biol. Chem., 279, 33946-33957.

Activating Compound

Activating Compound	Comment	Organism	Structure
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)

Cloned (Comment)	Organism
expression of C-terminally His-tagged enzyme in Escherichia coli BL21(DE3)	Homo sapiens
expression of isozyme IDP1 and IDP2 as His-tagged enzymes in a disruption mutant	Saccharomyces cerevisiae

Crystallization (Commentary)

Crystallization (Comment)	Organism
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 4°C, 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 20°C, X-ray diffraction structure determination and analysis	Homo sapiens

Crystallization (Comment)

Organism

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 4°C, 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 20°C, X-ray diffraction structure determination and analysis

Homo sapiens

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	kinetics of isozymes IDP1 and IDP2	Saccharomyces cerevisiae

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
cytosol	-	Homo sapiens	5829	-
cytosol	isozyme IDP2	Saccharomyces cerevisiae	5829	-
mitochondrion	isozyme IDP1	Saccharomyces cerevisiae	5739	-
peroxisome	isoyzme IDP3	Saccharomyces cerevisiae	5777	-

Metals/Ions

Metals/Ions	Comment	Organism
Ca2+	divalent metal ion is required, binding structure and conformation at the isocitrate-metal-binding site	Homo sapiens
Mg2+	-	Saccharomyces cerevisiae
Mg2+	divalent metal ion is required, binding structure and conformation at the isocitrate-metal-binding site	Homo sapiens

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
46381	-	x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry	Saccharomyces cerevisiae
46562	-	x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry	Saccharomyces cerevisiae
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)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
D-isocitrate + NADP+	Saccharomyces cerevisiae	the reaction is reversible for isozyme IDP2	2-oxoglutarate + CO2 + NADPH	-	r
isocitrate + NADP+	Homo sapiens	enzyme has a self-regulatory mechanism of activity mimicking the phosphorylation mechanism of bacterial enzymes	2-oxoglutarate + CO2 + NADPH + H+	-	?

Organism

Organism	UniProt	Comment	Textmining
Homo sapiens	-	-	-
Saccharomyces cerevisiae	-	1 cytosolic, 1 peroxisomal, and 1 mitochondrial isozyme	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography	Homo sapiens
recombinant His-tagged isozymes IDP1 and IDP2 by nickel affinity chromatography	Saccharomyces cerevisiae

Reaction

Reaction	Comment	Organism	Reaction ID
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	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
D-isocitrate + NADP+	the reaction is reversible for isozyme IDP2	Saccharomyces cerevisiae	2-oxoglutarate + CO2 + NADPH	-	r
isocitrate + NADP+	-	Homo sapiens	2-oxoglutarate + CO2 + NADPH + H+	-	?
isocitrate + NADP+	enzyme has a self-regulatory mechanism of activity mimicking the phosphorylation mechanism of bacterial enzymes	Homo sapiens	2-oxoglutarate + CO2 + NADPH + H+	-	?

Subunits

Subunits	Comment	Organism
?	x * 46381, isozyme IDP1, mass spectrometry, x * 46562, isozyme IDP2, mass spectrometry, x * 47856, isozyme IDP3, mass spectrometry	Saccharomyces cerevisiae
More	enzyme has 3 different conformational stages	Homo sapiens

Synonyms

Synonyms	Comment	Organism
IDP	-	Saccharomyces cerevisiae
NADP-dependent isocitrate dehydrogenase	-	Homo sapiens
NADP-dependent isocitrate dehydrogenase	-	Saccharomyces cerevisiae
NADP-IDH	-	Homo sapiens

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
6.5	-	assay at, reverse reaction	Saccharomyces cerevisiae
7.4	-	assay at	Homo sapiens
7.5	-	isozyme IDP2, forward reaction	Saccharomyces cerevisiae
8	-	isozyme IDP1, forward reaction	Saccharomyces cerevisiae

pH Range

pH Minimum	pH Maximum	Comment	Organism
6	9.5	-	Saccharomyces cerevisiae

Cofactor

Cofactor	Comment	Organism
NADP+	-	Saccharomyces cerevisiae
NADP+	binding site structure, interaction with the 2'-phosphate group of the ribose moiety	Homo sapiens
NADPH	-	Saccharomyces cerevisiae

pI Value

Organism	Comment	pI Value Maximum	pI Value
Saccharomyces cerevisiae	isozyme IDP2	-	5.5
Saccharomyces cerevisiae	isozyme IDP1	-	8.5
Saccharomyces cerevisiae	isozyme IDP3	-	10