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Literature summary extracted from

  • Romkina, A.; Kiriukhin, M.
    Biochemical and molecular characterization of the isocitrate dehydrogenase with dual coenzyme specificity from the obligate methylotroph Methylobacillus flagellatus (2017), PLoS ONE, 12, e0176056 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.41 expressed in Escherichia coli BL21(DE3) cells Methylobacillus flagellatus
1.1.1.42 expressed in Escherichia coli BL21(DE3) cells Methylobacillus flagellatus

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.1.1.41 Ca2+ complete inhibition at 2 mM (pH 6.0) Methylobacillus flagellatus
1.1.1.41 Cu2+ complete inhibition at 2 mM (pH 6.0) Methylobacillus flagellatus
1.1.1.41 additional information the enzyme is unaffected by the addition of 5 mM L-glutamate, L-glutamine, 2-oxoglutarate, oxaloacetate, cis-aconitate, citrate, pyruvate, malate, fumarate, succinate, CoA, AcCoA, NADH, and NADPH or 2 mM ADP and AMP Methylobacillus flagellatus
1.1.1.41 Zn2+ NAD+-linked activity at pH 8.5 is strongly inhibited by Zn2+ but partially restored at pH 6.0 Methylobacillus flagellatus
1.1.1.42 ATP
-
 Methylobacillus flagellatus
1.1.1.42 Ca2+ complete inhibition at 2 mM (pH 6.0) Methylobacillus flagellatus
1.1.1.42 Cu2+ complete inhibition at 2 mM (pH 6.0) Methylobacillus flagellatus
1.1.1.42 additional information the enzyme is unaffected by the addition of 5 mM L-glutamate, L-glutamine, 2-oxoglutarate, oxaloacetate, cis-aconitate, citrate, pyruvate, malate, fumarate, succinate, CoA, AcCoA, NADH, and NADPH or 2 mM ADP and AMP Methylobacillus flagellatus
1.1.1.42 Zn2+ NADP+-linked activity decreases by half at pH 6.0 Methylobacillus flagellatus

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.1.41 0.009
-
 isocitrate at pH 8.5 and 42°C Methylobacillus flagellatus
1.1.1.41 0.113
-
 NAD+ at pH 8.5 and 42°C Methylobacillus flagellatus
1.1.1.42 0.008
-
 isocitrate at pH 6.0 and 42°C Methylobacillus flagellatus
1.1.1.42 0.184
-
 NADP+ at pH 8.5 and 42°C Methylobacillus flagellatus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.1.1.41 Mg2+ Mg2+ can act as a significant substitute by providing up to 58-75% of the enzyme's maximal activity Methylobacillus flagellatus
1.1.1.41 Mn2+ Mn2+ enhances the activity the most effectively Methylobacillus flagellatus
1.1.1.42 Mg2+ Mg2+ can act as a significant substitute by providing up to 58-75% of the enzyme's maximal activity Methylobacillus flagellatus
1.1.1.42 Mn2+ Mn2+ enhances the activity the most effectively Methylobacillus flagellatus
1.1.1.42 Zn2+ NADP+-linked activity at pH 8.5 is fully activated by the presence of Zn2+ Methylobacillus flagellatus

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
1.1.1.41 83600
-
 gel filtration Methylobacillus flagellatus
1.1.1.42 83600
-
 gel filtration Methylobacillus flagellatus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.41 isocitrate + NAD+ Methylobacillus flagellatus
-
 2-oxoglutarate + CO2 + NADH + H+
-
 r
1.1.1.41 isocitrate + NAD+ Methylobacillus flagellatus ATCC51484
-
 2-oxoglutarate + CO2 + NADH + H+
-
 r
1.1.1.42 isocitrate + NADP+ Methylobacillus flagellatus
-
 2-oxoglutarate + CO2 + NADPH + H+
-
 r
1.1.1.42 isocitrate + NADP+ Methylobacillus flagellatus ATCC51484
-
 2-oxoglutarate + CO2 + NADPH + H+
-
 r

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.41 Methylobacillus flagellatus
-
-
-
1.1.1.41 Methylobacillus flagellatus ATCC51484
-
-
-
1.1.1.42 Methylobacillus flagellatus Q1GZD1
-
-
1.1.1.42 Methylobacillus flagellatus ATCC51484 Q1GZD1
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.41 Ni-NTA affinity resin column chromatography Methylobacillus flagellatus
1.1.1.42 Ni-NTA affinity resin column chromatography Methylobacillus flagellatus

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.41 isocitrate + APAD+ 55% activity compared to NAD+ Methylobacillus flagellatus 2-oxoglutarate + CO2 + APADH
-
 r
1.1.1.41 isocitrate + APAD+ 55% activity compared to NAD+ Methylobacillus flagellatus ATCC51484 2-oxoglutarate + CO2 + APADH
-
 r
1.1.1.41 isocitrate + NAD+
-
 Methylobacillus flagellatus 2-oxoglutarate + CO2 + NADH + H+
-
 r
1.1.1.41 isocitrate + NAD+ 100% activity Methylobacillus flagellatus 2-oxoglutarate + CO2 + NADH + H+
-
 r
1.1.1.41 isocitrate + NAD+
-
 Methylobacillus flagellatus ATCC51484 2-oxoglutarate + CO2 + NADH + H+
-
 r
1.1.1.41 isocitrate + NAD+ 100% activity Methylobacillus flagellatus ATCC51484 2-oxoglutarate + CO2 + NADH + H+
-
 r
1.1.1.41 isocitrate + NHD+ 4.0% activity compared to NAD+ Methylobacillus flagellatus 2-oxoglutarate + CO2 + NHDH
-
 r
1.1.1.41 isocitrate + NHD+ 4.0% activity compared to NAD+ Methylobacillus flagellatus ATCC51484 2-oxoglutarate + CO2 + NHDH
-
 r
1.1.1.42 isocitrate + APADP+ 60% activity compared to NAD+ Methylobacillus flagellatus 2-oxoglutarate + CO2 + APADPH
-
 r
1.1.1.42 isocitrate + APADP+ 60% activity compared to NAD+ Methylobacillus flagellatus ATCC51484 2-oxoglutarate + CO2 + APADPH
-
 r
1.1.1.42 isocitrate + NADP+
-
 Methylobacillus flagellatus 2-oxoglutarate + CO2 + NADPH + H+
-
 r
1.1.1.42 isocitrate + NADP+ 100% actiivty Methylobacillus flagellatus 2-oxoglutarate + CO2 + NADPH + H+
-
 r
1.1.1.42 isocitrate + NADP+
-
 Methylobacillus flagellatus ATCC51484 2-oxoglutarate + CO2 + NADPH + H+
-
 r
1.1.1.42 isocitrate + NADP+ 100% actiivty Methylobacillus flagellatus ATCC51484 2-oxoglutarate + CO2 + NADPH + H+
-
 r
1.1.1.42 isocitrate + NHDP+ 2.0% activity compared to NAD+ Methylobacillus flagellatus 2-oxoglutarate + CO2 + NHDPH
-
 r
1.1.1.42 isocitrate + NHDP+ 2.0% activity compared to NAD+ Methylobacillus flagellatus ATCC51484 2-oxoglutarate + CO2 + NHDPH
-
 r

Subunits

EC Number Subunits Comment Organism
1.1.1.41 homodimer 2 * 45000, SDS-PAGE Methylobacillus flagellatus
1.1.1.41 homodimer 2 * 44600, calculated from amino acid sequence Methylobacillus flagellatus
1.1.1.42 homodimer 2 * 45000, SDS-PAGE Methylobacillus flagellatus
1.1.1.42 homodimer 2 * 44600, calculated from amino acid sequence Methylobacillus flagellatus

Synonyms

EC Number Synonyms Comment Organism
1.1.1.41 IDH
-
 Methylobacillus flagellatus
1.1.1.41 NAD+-specific IDH
-
 Methylobacillus flagellatus
1.1.1.42 IDH
-
 Methylobacillus flagellatus
1.1.1.42 NADP+-specific IDH
-
 Methylobacillus flagellatus

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.1.1.41 60
-
-
 Methylobacillus flagellatus
1.1.1.42 60
-
-
 Methylobacillus flagellatus

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
1.1.1.41 50 75 the enzyme retains full activity at 50°C and loses ca. 50% of its activity after 1 h of incubation at 75°C Methylobacillus flagellatus
1.1.1.42 50 75 the enzyme retains full activity at 50°C and loses ca. 50% of its activity after 1 h of incubation at 75°C Methylobacillus flagellatus

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.1.41 166
-
 NAD+ at pH 8.5 and 42°C Methylobacillus flagellatus
1.1.1.42 56
-
 NADP+ at pH 8.5 and 42°C Methylobacillus flagellatus

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.1.1.41 8.5
-
-
 Methylobacillus flagellatus
1.1.1.42 6
-
-
 Methylobacillus flagellatus

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.41 NAD+ the catalytic efficiency for NAD+ is 5times higher for NAD+ than for NADP+ Methylobacillus flagellatus
1.1.1.42 NADP+ the catalytic efficiency for NAD+ is 5times higher for NAD+ than for NADP+ Methylobacillus flagellatus

pI Value

EC Number Organism Comment pI Value Maximum pI Value
1.1.1.41 Methylobacillus flagellatus isoelectric focusing
-
 5.5
1.1.1.41 Methylobacillus flagellatus calculated from amino acid sequence
-
 5.9
1.1.1.42 Methylobacillus flagellatus isoelectric focusing
-
 5.5
1.1.1.42 Methylobacillus flagellatus calculated from amino acid sequence
-
 5.9

IC50 Value

EC Number IC50 Value IC50 Value Maximum Comment Organism Inhibitor Structure
1.1.1.42 2
-
 at pH and °C Methylobacillus flagellatus ATP

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.1.1.41 1500
-
 NAD+ at pH 8.5 and 42°C Methylobacillus flagellatus
1.1.1.42 300
-
 NADP+ at pH 8.5 and 42°C Methylobacillus flagellatus