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Literature summary for 1.1.1.41 extracted from

  • Wang, P.; Lv, C.; Zhu, G.
    Novel type II and monomeric NAD+ specific isocitrate dehydrogenases: phylogenetic affinity, enzymatic characterization, and evolutionary implication (2015), Sci. Rep., 5, 9150.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
gene HMPREF1139_0890, sequence comparisons and phylogenetic analysis, recombinant overexpression of wild-type and mutant His6-tagged enzymes in Escherichia coli Campylobacter sp.
gene icd, sequence comparisons and phylogenetic analysis Campylobacter curvus
gene icd, sequence comparisons and phylogenetic analysis, recombinant overexpression of wild-type and mutant His6-tagged enzymes in Escherichia coli Ostreococcus sp. 'lucimarinus'
gene IDHP, sequence comparisons and phylogenetic analysis Micromonas commoda

Protein Variants

Protein Variants Comment Organism
D326R/M327H site-directed mutagenesis, the coenzyme specificity of the mutant CaIDH Asp326/Met327 is completely reversed from NAD+ to NADP+ Ostreococcus sp. 'lucimarinus'
D326X/M327X site-directed mutagenesis, the coenzyme specificity of the mutant OlIDH R326H327 is completely reversed from NAD+ to NADP+ Ostreococcus sp. 'lucimarinus'
L584H/D595R site-directed mutagenesis, the coenzyme specificity of the mutant CaIDH H584/R595 is completely reversed from NAD+ to NADP+ Campylobacter sp.

Inhibitors

Inhibitors Comment Organism Structure
Ca2+ complete inhibition at 2 mM Campylobacter sp.
Cu2+ complete inhibition at 2 mM Campylobacter sp.
Cu2+ complete inhibition at 2 mM Ostreococcus sp. 'lucimarinus'
Zn2+ complete inhibition at 2 mM Campylobacter sp.
Zn2+ complete inhibition at 2 mM Ostreococcus sp. 'lucimarinus'

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0082
-
NADP+ pH 75, 25°C, recombinant His6-tagged mutant D326R/M327H Ostreococcus sp. 'lucimarinus'
0.0114
-
NADP+ pH 75, 25°C, recombinant His6-tagged mutant L584H/D595R Campylobacter sp.
0.0289
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter sp.
0.0742
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter curvus
0.126
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Micromonas commoda
0.136
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Ostreococcus sp. 'lucimarinus'
0.476
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter curvus
0.493
-
NAD+ pH 75, 25°C, recombinant His6-tagged mutant L584H/D595R Campylobacter sp.
0.513
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter sp.
1.827
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Micromonas commoda
2.211
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Ostreococcus sp. 'lucimarinus'
2.948
-
NAD+ pH 75, 25°C, recombinant His6-tagged mutant D326R/M327H Ostreococcus sp. 'lucimarinus'

Metals/Ions

Metals/Ions Comment Organism Structure
Ca2+ activates, 13.6% activity compared to Mg2+ for OlIDH Ostreococcus sp. 'lucimarinus'
Co2+ activates, 35.5% activity compared to Mg2+ for CaIDH Campylobacter sp.
Mg2+ activates, 68.6% activity compared to Mg2+ for OlIDH Ostreococcus sp. 'lucimarinus'
Mg2+ activates, 78.3% activity compared to Mg2+ for CaIDH Campylobacter sp.
Mn2+ activates, Mn2+ is the most favorable cation for CaIDH Campylobacter sp.
Mn2+ activates, Mn2+ is the most favorable cation for OlIDH Ostreococcus sp. 'lucimarinus'
additional information divalent cations are required for activity Micromonas commoda
additional information divalent cations are required for activity Campylobacter curvus
additional information divalent cations are required for activity, low or poor activation by Co2+, Ni2+, K+, Na+, and Li+ Ostreococcus sp. 'lucimarinus'
additional information divalent cations are required for activity, low or poor activation by Rb+, Ni2+, K+, Na+, and Li+ Campylobacter sp.
Rb+ activates, 11.0% activity compared to Mg2+ for OlIDH Ostreococcus sp. 'lucimarinus'

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
45000
-
-
Ostreococcus sp. 'lucimarinus'
80000
-
-
Campylobacter sp.
81000
-
recombinant His6-tagged enzyme, gel filtration Campylobacter sp.
92000
-
recombinant His6-tagged enzyme, gel filtration Ostreococcus sp. 'lucimarinus'

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
isocitrate + NAD+ Ostreococcus sp. 'lucimarinus'
-
2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+ Micromonas commoda
-
2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+ Campylobacter sp.
-
2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+ Campylobacter curvus
-
2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+ Campylobacter curvus 525.92
-
2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+ Campylobacter sp. FOBRC14
-
2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+ Micromonas commoda RCC299
-
2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+ Ostreococcus sp. 'lucimarinus' CCE9901
-
2-oxoglutarate + CO2 + NADH + H+
-
?

Organism

Organism UniProt Comment Textmining
Campylobacter curvus A0A0M4S9Q1
-
-
Campylobacter curvus 525.92 A0A0M4S9Q1
-
-
Campylobacter sp. J4X756
-
-
Campylobacter sp. FOBRC14 J4X756
-
-
Micromonas commoda C1E5X2
-
-
Micromonas commoda RCC299 C1E5X2
-
-
Ostreococcus sp. 'lucimarinus'
-
-
-
Ostreococcus sp. 'lucimarinus' A4SBK5
-
-
Ostreococcus sp. 'lucimarinus' CCE9901
-
-
-
Ostreococcus sp. 'lucimarinus' CCE9901 A4SBK5
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant wild-type and mutant His6-tagged enzymes from Escherichia coli Campylobacter sp.
recombinant wild-type and mutant His6-tagged enzymes from Escherichia coli Ostreococcus sp. 'lucimarinus'

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
3.8
-
purified recombinant His6-tagged enzyme, pH 7.5, 25°C, with NADP+ Ostreococcus sp. 'lucimarinus'
8.7
-
purified recombinant His6-tagged enzyme, pH 7.5, 25°C, with NADP+ Campylobacter sp.
53.2
-
purified recombinant His6-tagged enzyme, pH 7.5, 25°C, with NAD+ Campylobacter sp.
72.3
-
purified recombinant His6-tagged enzyme, pH 7.5, 25°C, with NAD+ Ostreococcus sp. 'lucimarinus'

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
isocitrate + NAD+
-
Ostreococcus sp. 'lucimarinus' 2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+
-
Micromonas commoda 2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+
-
Campylobacter sp. 2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+
-
Campylobacter curvus 2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+
-
Campylobacter curvus 525.92 2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+
-
Campylobacter sp. FOBRC14 2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+
-
Micromonas commoda RCC299 2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+
-
Ostreococcus sp. 'lucimarinus' CCE9901 2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NADP+ very low activity Micromonas commoda 2-oxoglutarate + CO2 + NADPH + H+
-
?
isocitrate + NADP+ very low activity Campylobacter sp. 2-oxoglutarate + CO2 + NADPH + H+
-
?
isocitrate + NADP+ very low activity Campylobacter curvus 2-oxoglutarate + CO2 + NADPH + H+
-
?
isocitrate + NADP+ very low activity Ostreococcus sp. 'lucimarinus' 2-oxoglutarate + CO2 + NADPH + H+
-
?
isocitrate + NADP+ very low activity Campylobacter curvus 525.92 2-oxoglutarate + CO2 + NADPH + H+
-
?
isocitrate + NADP+ very low activity Campylobacter sp. FOBRC14 2-oxoglutarate + CO2 + NADPH + H+
-
?
isocitrate + NADP+ very low activity Micromonas commoda RCC299 2-oxoglutarate + CO2 + NADPH + H+
-
?
isocitrate + NADP+ very low activity Ostreococcus sp. 'lucimarinus' CCE9901 2-oxoglutarate + CO2 + NADPH + H+
-
?

Subunits

Subunits Comment Organism
homodimer
-
Ostreococcus sp. 'lucimarinus'
homodimer
-
Micromonas commoda
homodimer 2 * 45000, recombinant His6-tagged enzyme, SDS-PAGE Ostreococcus sp. 'lucimarinus'
monomer
-
Campylobacter curvus
monomer 1 * 80000, recombinant His6-tagged enzyme, SDS-PAGE Campylobacter sp.

Synonyms

Synonyms Comment Organism
CaIDH
-
Campylobacter sp.
CcIDH
-
Campylobacter curvus
MiIDH
-
Micromonas commoda
monomeric NAD-IDH
-
Campylobacter sp.
monomeric NAD-IDH
-
Campylobacter curvus
OlIDH
-
Ostreococcus sp. 'lucimarinus'
type II homodimeric NAD-IDH
-
Ostreococcus sp. 'lucimarinus'
type II homodimeric NAD-IDH
-
Micromonas commoda

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
assay at Micromonas commoda
25
-
assay at Campylobacter curvus
40
-
with Mn2+ Campylobacter sp.
40
-
with Mg2+ or Mn2+ Ostreococcus sp. 'lucimarinus'
45
-
with Mg2+ Campylobacter sp.

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
40 55 recombinant CaIDH retains the majority of the activity below 45°C, its activity drops rapidly as the temperature is raised. Incubation at 55°C for 20 min causes a 55% or 75% loss of activity in the presence of Mg2+ or Mn2+, respectively Campylobacter sp.
45 50 recombinant OlIDH is stable below 45°C, but its activity rapidly declines as the temperature is raised. Incubation at 45°C for 20 min causes a 28% or 21% loss of activity in the presence of Mg2+ or Mn2+, respectively, whereas incubation at 50°C causes a 91% or 84% loss of activity in the presence of Mg2+ or Mn2+, respectively Ostreococcus sp. 'lucimarinus'

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.4
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Micromonas commoda
1.8
-
NADP+ pH 75, 25°C, recombinant His6-tagged mutant D326R/M327H Ostreococcus sp. 'lucimarinus'
1.9
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter sp.
2
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter curvus
4.2
-
NADP+ pH 75, 25°C, recombinant His6-tagged mutant L584H/D595R Campylobacter sp.
7
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter sp.
9.5
-
NAD+ pH 75, 25°C, recombinant His6-tagged mutant L584H/D595R Campylobacter sp.
10
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Ostreococcus sp. 'lucimarinus'
10.8
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter curvus
22.5
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Micromonas commoda
29.1
-
NAD+ pH 75, 25°C, recombinant His6-tagged mutant D326R/M327H Ostreococcus sp. 'lucimarinus'
60.6
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Ostreococcus sp. 'lucimarinus'

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
assay at Micromonas commoda
7.5
-
assay at Campylobacter curvus
7.5
-
with Mn2+ Campylobacter sp.
8
-
with Mg2+ Campylobacter sp.
8.5
-
with Mn2+ Ostreococcus sp. 'lucimarinus'
9
-
with Mg2+ Ostreococcus sp. 'lucimarinus'

Cofactor

Cofactor Comment Organism Structure
NAD+ specific for, the enzyme displays 224fold preference for NAD+ over NADP+ Micromonas commoda
NAD+ specific for, the enzyme displays 37fold preference for NAD+ over NADP+ Campylobacter curvus
NAD+ specific for, the enzyme displays 61fold preference for NAD+ over NADP+. Putative coenzyme discriminating amino acids residues are Leu584 and Asp595 in CaIDH Campylobacter sp.
NAD+ specific for, the enzyme displays 99fold preference for NAD+ over NADP+ Ostreococcus sp. 'lucimarinus'
NAD+ specific for, the enzyme displays 99fold preference for NAD+ over NADP+. Putative coenzyme discriminating amino acids residues are Asp326 and Met327 in OlIDH Ostreococcus sp. 'lucimarinus'

General Information

General Information Comment Organism
evolution evolutionary relationships of IDHs, overview Ostreococcus sp. 'lucimarinus'
evolution evolutionary relationships of IDHs, overview. The enzyme belongs to the IDH enzyme family and is clustered into a unique clade among the type II subfamily Ostreococcus sp. 'lucimarinus'
evolution evolutionary relationships of IDHs, overview. The enzyme belongs to the IDH enzyme family and the subclade of monomeric enzymes Campylobacter sp.
evolution evolutionary relationships of IDHs, overview. The enzyme belongs to the IDH enzyme family and the subclade of monomeric enzymes Campylobacter curvus
evolution evolutionary relationships of IDHs, phylogenetic analysis, overview. The enzyme belongs to the IDH enzyme family and the subclade of type II homodimeric enzymes Micromonas commoda
metabolism NAD-IDH is a key enzyme in the tricarboxylic acid cycle. It catalyzes the oxidative decarboxylation of isocitrate to 2-oxoglutarate and CO2, which is accompanied by the reduction of NAD+ to NADH. The IDH reaction provides organisms with not only energy but also biosynthetic precursors, such as 2-oxoglutarate, for metabolism Micromonas commoda
metabolism NAD-IDH is a key enzyme in the tricarboxylic acid cycle. It catalyzes the oxidative decarboxylation of isocitrate to 2-oxoglutarate and CO2, which is accompanied by the reduction of NAD+ to NADH. The IDH reaction provides organisms with not only energy but also biosynthetic precursors, such as 2-oxoglutarate, for metabolism Campylobacter sp.
metabolism NAD-IDH is a key enzyme in the tricarboxylic acid cycle. It catalyzes the oxidative decarboxylation of isocitrate to 2-oxoglutarate and CO2, which is accompanied by the reduction of NAD+ to NADH. The IDH reaction provides organisms with not only energy but also biosynthetic precursors, such as 2-oxoglutarate, for metabolism Campylobacter curvus
metabolism NAD-IDH is a key enzyme in the tricarboxylic acid cycle. It catalyzes the oxidative decarboxylation of isocitrate to 2-oxoglutarate and CO2, which is accompanied by the reduction of NAD+ to NADH. The IDH reaction provides organisms with not only energy but also biosynthetic precursors, such as 2-oxoglutarate, for metabolism Ostreococcus sp. 'lucimarinus'

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.8
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Micromonas commoda
4
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter sp.
4
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter curvus
4.5
-
NADP+ pH 75, 25°C, recombinant His6-tagged enzyme Ostreococcus sp. 'lucimarinus'
10
-
NAD+ pH 75, 25°C, recombinant His6-tagged mutant D326R/M327H Ostreococcus sp. 'lucimarinus'
19.3
-
NAD+ pH 75, 25°C, recombinant His6-tagged mutant L584H/D595R Campylobacter sp.
146
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter curvus
179
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Micromonas commoda
220
-
NADP+ pH 75, 25°C, recombinant His6-tagged mutant D326R/M327H Ostreococcus sp. 'lucimarinus'
242
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Campylobacter sp.
368
-
NADP+ pH 75, 25°C, recombinant His6-tagged mutant L584H/D595R Campylobacter sp.
444
-
NAD+ pH 75, 25°C, recombinant His6-tagged enzyme Ostreococcus sp. 'lucimarinus'