BRENDA - Enzyme Database

Cysteine is the general base that serves in catalysis by isocitrate lyase and in mechanism-based inhibition by 3-nitropropionate

Moynihan, M.M.; Murkin, A.S.; Biochemistry 53, 178-187 (2014)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
4.1.3.1
expression of the enzyme with a thrombin-cleavable N-terminal His6 tag in Escherichia coli strain BL21(DE3)
Mycobacterium tuberculosis
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
4.1.3.1
3-nitropropionate
a succinate analogue. Inhibition by 3-nitropropionate proceeds through an unusual double slow-onset process featuring formation of a complex with a Ki of 0.0033 mM during the first minute, followed by formation of a final complex with a Ki* of 44 nM over the course of several min to hours
Mycobacterium tuberculosis
4.1.3.1
glyoxylate
-
Mycobacterium tuberculosis
4.1.3.1
Itaconate
a succinate analogue lacking an acidic alpha-proton, the inhhibitor does not display slow-binding behavior
Mycobacterium tuberculosis
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.1.3.1
additional information
-
additional information
stopped-flow spectroscopy and steady-state kinetics, solvent kinetic isotope effects, overview. Whereas the D2OV is consistent with partially rate-limiting proton transfer during formation of the hydroxyl group of isocitrate, the large inverse D2O(V/Ksuccinate) indicates that substantially different kinetic parameters exist when the enzyme is saturated with succinate
Mycobacterium tuberculosis
4.1.3.1
0.045
-
isocitrate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
4.1.3.1
0.14
-
glyoxylate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
4.1.3.1
0.412
-
succinate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
4.1.3.1
Mg2+
required
Mycobacterium tuberculosis
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
4.1.3.1
isocitrate
Mycobacterium tuberculosis
-
succinate + glyoxylate
-
-
r
4.1.3.1
isocitrate
Mycobacterium tuberculosis H37R
-
succinate + glyoxylate
-
-
r
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
4.1.3.1
Mycobacterium tuberculosis
-
-
-
4.1.3.1
Mycobacterium tuberculosis H37R
-
-
-
Purification (Commentary)
EC Number
Commentary
Organism
4.1.3.1
recombinant N-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nicke affinity chromatography, cleavage of the His-tag by thrombin, and dialysis
Mycobacterium tuberculosis
Reaction
EC Number
Reaction
Commentary
Organism
4.1.3.1
isocitrate = succinate + glyoxylate
common mechanism for catalysis with succinate: (1) an unfavorable prebinding isomerization of the active site Cys191-His193 pair to the thiolate-imidazolium form, a process that is favored in D2O, and (2) the transfer of a proton from succinate or 3-NP to Cys191
Mycobacterium tuberculosis
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4.1.3.1
isocitrate
-
727045
Mycobacterium tuberculosis
succinate + glyoxylate
-
-
-
r
4.1.3.1
isocitrate
-
727045
Mycobacterium tuberculosis H37R
succinate + glyoxylate
-
-
-
r
4.1.3.1
succinate + glyoxylate
-
727045
Mycobacterium tuberculosis
isocitrate
-
-
-
r
4.1.3.1
succinate + glyoxylate
-
727045
Mycobacterium tuberculosis H37R
isocitrate
-
-
-
r
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
4.1.3.1
37
-
assay at
Mycobacterium tuberculosis
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.1.3.1
8.5
-
succinate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
4.1.3.1
12.2
-
isocitrate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
4.1.3.1
7
-
assay at
Mycobacterium tuberculosis
Ki Value [mM]
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
4.1.3.1
additional information
-
additional information
solvent isotope effects in inhibition by itaconate and 3-nitropropionate, overview
Mycobacterium tuberculosis
4.1.3.1
4.3
-
glyoxylate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
4.1.3.1
expression of the enzyme with a thrombin-cleavable N-terminal His6 tag in Escherichia coli strain BL21(DE3)
Mycobacterium tuberculosis
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
4.1.3.1
3-nitropropionate
a succinate analogue. Inhibition by 3-nitropropionate proceeds through an unusual double slow-onset process featuring formation of a complex with a Ki of 0.0033 mM during the first minute, followed by formation of a final complex with a Ki* of 44 nM over the course of several min to hours
Mycobacterium tuberculosis
4.1.3.1
glyoxylate
-
Mycobacterium tuberculosis
4.1.3.1
Itaconate
a succinate analogue lacking an acidic alpha-proton, the inhhibitor does not display slow-binding behavior
Mycobacterium tuberculosis
Ki Value [mM] (protein specific)
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
4.1.3.1
additional information
-
additional information
solvent isotope effects in inhibition by itaconate and 3-nitropropionate, overview
Mycobacterium tuberculosis
4.1.3.1
4.3
-
glyoxylate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.1.3.1
additional information
-
additional information
stopped-flow spectroscopy and steady-state kinetics, solvent kinetic isotope effects, overview. Whereas the D2OV is consistent with partially rate-limiting proton transfer during formation of the hydroxyl group of isocitrate, the large inverse D2O(V/Ksuccinate) indicates that substantially different kinetic parameters exist when the enzyme is saturated with succinate
Mycobacterium tuberculosis
4.1.3.1
0.045
-
isocitrate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
4.1.3.1
0.14
-
glyoxylate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
4.1.3.1
0.412
-
succinate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
4.1.3.1
Mg2+
required
Mycobacterium tuberculosis
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
4.1.3.1
isocitrate
Mycobacterium tuberculosis
-
succinate + glyoxylate
-
-
r
4.1.3.1
isocitrate
Mycobacterium tuberculosis H37R
-
succinate + glyoxylate
-
-
r
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
4.1.3.1
recombinant N-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nicke affinity chromatography, cleavage of the His-tag by thrombin, and dialysis
Mycobacterium tuberculosis
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4.1.3.1
isocitrate
-
727045
Mycobacterium tuberculosis
succinate + glyoxylate
-
-
-
r
4.1.3.1
isocitrate
-
727045
Mycobacterium tuberculosis H37R
succinate + glyoxylate
-
-
-
r
4.1.3.1
succinate + glyoxylate
-
727045
Mycobacterium tuberculosis
isocitrate
-
-
-
r
4.1.3.1
succinate + glyoxylate
-
727045
Mycobacterium tuberculosis H37R
isocitrate
-
-
-
r
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
4.1.3.1
37
-
assay at
Mycobacterium tuberculosis
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.1.3.1
8.5
-
succinate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
4.1.3.1
12.2
-
isocitrate
recombinant detagged enzyme, pH 7.0, 37°C
Mycobacterium tuberculosis
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
4.1.3.1
7
-
assay at
Mycobacterium tuberculosis
General Information
EC Number
General Information
Commentary
Organism
4.1.3.1
physiological function
the enzyme catalyzes the first committed step in the glyoxylate cycle, it is essential in Mycobacterium tuberculosis for cell survival during chronic infection
Mycobacterium tuberculosis
General Information (protein specific)
EC Number
General Information
Commentary
Organism
4.1.3.1
physiological function
the enzyme catalyzes the first committed step in the glyoxylate cycle, it is essential in Mycobacterium tuberculosis for cell survival during chronic infection
Mycobacterium tuberculosis