Information on EC 1.1.1.286 - isocitrate-homoisocitrate dehydrogenase

for references in articles please use BRENDA:EC1.1.1.286
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The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota

EC NUMBER
COMMENTARY hide
1.1.1.286
-
RECOMMENDED NAME
GeneOntology No.
isocitrate-homoisocitrate dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH + H+
show the reaction diagram
isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
coenzyme B biosynthesis
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L-glutamine biosynthesis III
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L-lysine biosynthesis IV
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L-lysine biosynthesis V
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TCA cycle II (plants and fungi)
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TCA cycle III (animals)
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lysine metabolism
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Citrate cycle (TCA cycle)
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Lysine biosynthesis
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Metabolic pathways
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Biosynthesis of secondary metabolites
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Microbial metabolism in diverse environments
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Biosynthesis of antibiotics
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SYSTEMATIC NAME
IUBMB Comments
isocitrate(homoisocitrate):NAD+ oxidoreductase (decarboxylating)
Requires Mn2+ and K+ or NH4+ for activity. Unlike EC 1.1.1.41, isocitrate dehydrogenase (NAD+) and EC 1.1.1.87, homoisocitrate dehydrogenase, this enzyme, from Pyrococcus horikoshii, can use both isocitrate and homoisocitrate as substrates. The enzyme may play a role in both the lysine and glutamate biosynthesis pathways.
CAS REGISTRY NUMBER
COMMENTARY hide
9001-58-5
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9067-90-7
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
expression in Escherichia coli
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Manually annotated by BRENDA team
Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039
expression in Escherichia coli
Swissprot
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+
2-oxoadipate + CO2 + NADH + H+
show the reaction diagram
-
chemical mechanism, stereochemistry of hydride transfer to NAD, overview
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-
?
3-isopropylmalate + NAD+
2-oxoisocaproate + CO2 + NADH + H+
show the reaction diagram
3-isopropylmalate + NAD+
?
show the reaction diagram
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at 0.1% of the rate with homoisocitrate
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-
?
homoisocitrate + NAD+
2-oxoadipate + CO2 + NADH + H+
show the reaction diagram
homoisocitrate + NAD+
? + NADH
show the reaction diagram
homoisocitrate + NADP+
2-oxoadipate + CO2 + NADPH + H+
show the reaction diagram
isocitrate + NAD+
2-oxoglutarate + CO2 + NADH
show the reaction diagram
isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
homoisocitrate + NAD+
2-oxoadipate + CO2 + NADH + H+
show the reaction diagram
homoisocitrate + NAD+
? + NADH
show the reaction diagram
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-
-
-
?
homoisocitrate + NADP+
2-oxoadipate + CO2 + NADPH + H+
show the reaction diagram
isocitrate + NAD+
2-oxoglutarate + CO2 + NADH
show the reaction diagram
isocitrate + NADP+
2-oxoglutarate + CO2 + NADPH
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADH
NADH forms specific contacts with enzyme TtHICDH. The 2'- and 3-OHs of the adenine ribose of NADH form hydrogen bonds with Asp265 conserved among HICDHs, which may serve as a determinant for the preference of HICDH family members for NAD+ to NADP+
NADP+
Saci_2375 is an NADP+-dependent enzyme with the ability to function as ICDH, EC 1.1.1.42, and HICDH, EC 1.1.1.87
NADPH
Saci_2375 is an NADP+-dependent enzyme with the ability to function as ICDH, EC 1.1.1.42, and HICDH, EC 1.1.1.87
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
NH4+
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200 mM activates by 80.9%
Rb+
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200 mM activates by 29.3%
additional information
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200 mM Cs+, Li+, and Na+ do not activate
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2S,3S)-thiahomoisocitrate
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3-carboxypropylidenemalate
homoisocitrate
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competitive, pH-dependent substrate inhibition
isocitrate
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competitive, pH-dependent substrate inhibition
K+
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absolute requirement, inhibitory above 0.4 M
Mn2+
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inhibitory above 1 mM
NADH
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product inhibitor
NH4+
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may substitute for K+, inhibitory above 0.2 M
potassium acetate
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.05 - 1.33
3-isopropylmalate
0.0073 - 7.486
homoisocitrate
0.014 - 2.2
isocitrate
0.036 - 1.8
NAD+
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.371 - 9.4
3-isopropylmalate
4.8 - 171
homoisocitrate
0.22 - 171
isocitrate
21.8 - 30.3
NAD+
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.2 - 46
3-isopropylmalate
5.3 - 3364
homoisocitrate
0.44 - 2259
isocitrate
0.56 - 470
NAD+
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.043
3-carboxypropylidenemalate
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pH 8.0, 25°C, versus homoisocitrate
500
potassium acetate
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 10
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pH-profile, overview
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35727
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4 * 35751, mass spectrometry, 4 * 35727, calculated
35751
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4 * 35751, mass spectrometry, 4 * 35727, calculated
154000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant His6-tagged enzyme in apoform or in complex with substrates isocitrate, homoisocitrate, and 3-isopropylmalate, hanging drop vapour diffusion method, for the apoenzyme: mixing of 0.001 ml of 10 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 150 mM NaCl, with 0.001 ml of reservoir solution containing 100 mM imidazole-HCl, pH 6.5, and 2.3 M NaCl, equilibration against 1 m of reservoir solution, at 20°C, for the ternary complex with homoisocitrate and Mn2+: mixing of 0.0015 ml of 10 mg/ml protein in 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 10% glycerol, 1 mM MnSO4, and 5 mM homoisocitrate, with 0.0015 ml of reservoir solution containing 100 mM HEPES-NaOH, pH 7.5, 200 mM NaCl, and 10% v/v 2-propanol, at 20°C, for the ternary complex with homoisocitrate and Mn2+: mixing of 0.0015 ml of 5 mg/ml protein in 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 10% glycerol, 1 mM MnSO4, and 5 mM isocitrate, with 0.0015 ml of reservoir solution containing 100 mM Tris–HCl, pH 7.5, 200 mM NaCl, and 30% v/v 2-methyl-2,4-pentanediol, at 20°C, and for the ternary complex with 3-isopropylmalate and Mn2+: mixing of 0.001 ml of 15 mg/ml protein in 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 10% glycerol, 1 mM MnSO4, and 5 mM 3-isopropylmalate, with 0.001 ml of reservoir solution containing 100 mM HEPES-NaOH, pH 7.5, 200 mM NaCl, and 36% v/v 2-methyl-2,4-pentanediol, at 20°C, X-ray diffraction structure determination and analysis at 1.7 A resolution for the apoenzyme, and at 2.50-2.64 A resolution for the complexed enzyme
purified enzyme TtHICDH in quaternary complex with homoisocitrate, NADH, and Mg2+, X-ray diffraction strczure determination and analysis at 2.5 A resolution, molecular replacement using the apoform of TtHICDH, PDB ID 1X0L, at a resolution of 2.5 A
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
90
half-life 16.7 h
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme expressed in Escherichia coli, purification of inclusion bodies requires N-laurylsarcosine
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recombinant enzyme from Escherichia coli by anion exchange chromatography, ammonium sufate fractionation, hydrophobic interaction chromatography, and gel filtration
recombinant enzyme from Escherichia coli strain BL21(DE3)Codon-Plus-RIL b anion exchange chromatography, ammonium sulfate fractionation, hydropobic interaction chromatography, ultrafiltration, and gel filtration
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21-CodonPlus (DE3)-RIL by nickel affinity chromatography and gel filtration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
gene saci_2375, DNA and amino acid sequence determination and analysis, recombinant expression in Escherichia coli strain BL21(DE3)Codon-Plus-RIL
gene TK0280, phylogenetic analysis and tree, cloning in Escherichia coli strain DH5alpha, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21-CodonPlus (DE3)-RIL
recombinant expression in Escherichia coli strain Escherichia coli BL21(DE3)CodonPlus-RIL
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
R85V
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increased ability to use 3-isopropylmalate
R87T
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uses substrate homoisocitrate, but not substrates isocitrate or 3-isopropylmalate
R87V
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uses substrate homoisocitrate, but not substrates isocitrate or 3-isopropylmalate
I82N
site-directed mutagenesis, the mutant shows reduced activity and altered substrate specificity compared to the wild-type enzyme
L81P
site-directed mutagenesis, the mutant shows reduced activity and altered substrate specificity compared to the wild-type enzyme
L83R
site-directed mutagenesis, the mutant shows reduced activity and altered substrate specificity compared to the wild-type enzyme
S80A
site-directed mutagenesis, the mutant shows reduced activity and altered substrate specificity compared to the wild-type enzyme
T71V
site-directed mutagenesis, the mutant shows reduced activity and altered substrate specificity compared to the wild-type enzyme
I82N
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site-directed mutagenesis, the mutant shows reduced activity and altered substrate specificity compared to the wild-type enzyme
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L81P
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site-directed mutagenesis, the mutant shows reduced activity and altered substrate specificity compared to the wild-type enzyme
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S80A
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site-directed mutagenesis, the mutant shows reduced activity and altered substrate specificity compared to the wild-type enzyme
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T71V
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site-directed mutagenesis, the mutant shows reduced activity and altered substrate specificity compared to the wild-type enzyme
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additional information