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Literature summary for 1.1.1.41 extracted from

  • Huang, S.P.; Zhou, L.C.; Wen, B.; Wang, P.; Zhu, G.P.
    Biochemical characterization and crystal structure of a novel NAD+-dependent isocitrate dehydrogenase from Phaeodactylum tricornutum (2020), Int. J. Mol. Sci., 21, 5915 .
    View publication on PubMedView publication on EuropePMC

Activating Compound

Activating Compound Comment Organism Structure
citrate 106.29% activity at 1 mM Phaeodactylum tricornutum

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli Rosetta (DE3) cells Phaeodactylum tricornutum

Crystallization (Commentary)

Crystallization (Comment) Organism
sitting drop vapor diffusion method, using 200 mM NaCl, 100 mM sodium HEPES (pH 7.5), and 25% (w/v) PEG 4000 Phaeodactylum tricornutum

Protein Variants

Protein Variants Comment Organism
D459A/N461A/D463A/F465A the mutant maintains comparable specific activity to that of wild type enzyme Phaeodactylum tricornutum
IDH1-EF the mutant without the EF-hand domain (deleted Gln424-Val495 in a total of 72 residues) completely lost its catalytic activity Phaeodactylum tricornutum

Inhibitors

Inhibitors Comment Organism Structure
ADP 86.63% residual activity at 1 mM Phaeodactylum tricornutum
AMP 97.88% residual activity at 1 mM Phaeodactylum tricornutum
ATP 88.7% residual activity at 1 mM Phaeodactylum tricornutum
Ca2+ 3.87% residual activity at 2 mM Phaeodactylum tricornutum
Co2+ 5.96% residual activity at 2 mM Phaeodactylum tricornutum
Cu2+ 5.76% residual activity at 2 mM Phaeodactylum tricornutum
K+ 4.12% residual activity at 2 mM Phaeodactylum tricornutum
Li+ 5.15% residual activity at 2 mM Phaeodactylum tricornutum
additional information not inhibited by 2-oxoglutarate Phaeodactylum tricornutum
Na+ 4.66% residual activity at 2 mM Phaeodactylum tricornutum
NADH competitive inhibitor Phaeodactylum tricornutum
Ni2+ 1.6% residual activity at 2 mM Phaeodactylum tricornutum

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.903
-
NAD+ in the presence of Mg2+, at pH 8.0 and 25°C Phaeodactylum tricornutum
1.1325
-
NAD+ in the presence of Mn2+, at pH 8.0 and 25°C Phaeodactylum tricornutum

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ 2 mM used in assay conditions Phaeodactylum tricornutum
Mn2+ 2 mM used in assay conditions Phaeodactylum tricornutum

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
110000
-
gel filtration Phaeodactylum tricornutum

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
isocitrate + NAD+ Phaeodactylum tricornutum
-
2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+ Phaeodactylum tricornutum FACHB-2174
-
2-oxoglutarate + CO2 + NADH + H+
-
?

Organism

Organism UniProt Comment Textmining
Phaeodactylum tricornutum
-
-
-
Phaeodactylum tricornutum FACHB-2174
-
-
-

Purification (Commentary)

Purification (Comment) Organism
Co2+ affinity column chromatography Phaeodactylum tricornutum

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
78
-
mutant enzyme D459A/N461A/D463A/F465A, in the presence of Mn2+, at pH 8.0 and 25°C Phaeodactylum tricornutum
87.1
-
wild type enzyme, in the presence of Mn2+, at pH 8.0 and 25°C Phaeodactylum tricornutum

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
isocitrate + NAD+
-
Phaeodactylum tricornutum 2-oxoglutarate + CO2 + NADH + H+
-
?
isocitrate + NAD+
-
Phaeodactylum tricornutum FACHB-2174 2-oxoglutarate + CO2 + NADH + H+
-
?
additional information the enzyme has no detectable activity with NADP+ Phaeodactylum tricornutum ?
-
-
additional information the enzyme has no detectable activity with NADP+ Phaeodactylum tricornutum FACHB-2174 ?
-
-

Subunits

Subunits Comment Organism
homodimer 2 * 55000, His6-tagged enzyme, SDS-PAGE Phaeodactylum tricornutum
homodimer 2 * 55100, calculated from amino acid sequence Phaeodactylum tricornutum

Synonyms

Synonyms Comment Organism
IDH1
-
Phaeodactylum tricornutum
NAD+-dependent isocitrate dehydrogenase
-
Phaeodactylum tricornutum
NAD-IDH
-
Phaeodactylum tricornutum

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
-
with Mn2+ Phaeodactylum tricornutum
35
-
with Mg2+ Phaeodactylum tricornutum

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
28 35 the enzyme is stable below 28°C, but rapidly loses activity above 30°C, and 60% activity remains after a 20 min incubation at 35°C Phaeodactylum tricornutum

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
79
-
NAD+ in the presence of Mg2+, at pH 8.0 and 25°C Phaeodactylum tricornutum
180.5
-
NAD+ in the presence of Mn2+, at pH 8.0 and 25°C Phaeodactylum tricornutum

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
with Mn2+ Phaeodactylum tricornutum
8.8
-
with Mg2+ Phaeodactylum tricornutum

Cofactor

Cofactor Comment Organism Structure
NAD+
-
Phaeodactylum tricornutum

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.45
-
NADH at pH 8.0 and 25°C Phaeodactylum tricornutum

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
90
-
NAD+ in the presence of Mg2+, at pH 8.0 and 25°C Phaeodactylum tricornutum
160
-
NAD+ in the presence of Mn2+, at pH 8.0 and 25°C Phaeodactylum tricornutum