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Literature summary for 3.7.1.1 extracted from

  • Narayanan, B.; Niu, W.; Joosten, H.J.; Li, Z.; Kuipers, R.K.; Schaap, P.J.; Dunaway-Mariano, D.; Herzberg, O.
    Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member (2009), J. Mol. Biol., 386, 486-503.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli BL21(DE3) cells Aspergillus niger

Crystallization (Commentary)

Crystallization (Comment) Organism
DMML in complex with Mg2+ and in complex with Mg2+ and 3,3-difluorooxalacetate, hanging drop vapor diffusion method, using 0.2 M potassium thiocyanate, 0.1 M bis-Tris propane (pH 7.5), and 20k polyethylene glycol 3350, or using 14k polyethylene glycol 6000 and 0.1 M MES (pH 6.5) Aspergillus niger

Protein Variants

Protein Variants Comment Organism
C124A the mutant shows decreased kcat compared to the wild type enzyme Aspergillus niger
C124S the mutant shows decreased kcat compared to the wild type enzyme Aspergillus niger
D59A the mutant shows decreased kcat compared to the wild type enzyme Aspergillus niger
D59S the mutant shows decreased kcat compared to the wild type enzyme Aspergillus niger
P240S the mutant shows decreased kcat compared to the wild type enzyme Aspergillus niger
P240T the mutant shows decreased kcat compared to the wild type enzyme Aspergillus niger

Inhibitors

Inhibitors Comment Organism Structure
3,3-difluoroxaloacetate tight binding competitive inhibitor Aspergillus niger
additional information (2R,3S)-isocitrate, (R)-malate, (S)-malate, and carboxyphosphoenolpyruvate are not inhibitors Aspergillus niger
oxalate weak binding competitive inhibitor Aspergillus niger
Phosphonopyruvate
-
Aspergillus niger

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.027
-
oxaloacetate mutant enzyme C124S, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
0.22
-
oxaloacetate wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
0.234
-
oxaloacetate wild type enzyme, in 0.1 M imidazole (pH 7.6 and 25°C) Aspergillus niger
1.11
-
oxaloacetate mutant enzyme P240S, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
1.22
-
oxaloacetate mutant enzyme P240T, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
20.14
-
oxaloacetate mutant enzyme C124A, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required for activity (5 mM) Aspergillus niger

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
31986
-
4 * 31986, mass spectrometry Aspergillus niger
32000
-
4 * 32000, SDS-PAGE Aspergillus niger
32117
-
4 * 32117, calculated from amino acid sequence Aspergillus niger
110000
-
gel filtration Aspergillus niger

Organism

Organism UniProt Comment Textmining
Aspergillus niger
-
-
-

Purification (Commentary)

Purification (Comment) Organism
Q-Sepharose column chromatography, ammonium sulfate precipitation, butyl Sepharose column chromatography, and phenyl Sepharose column chromatography Aspergillus niger

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
oxaloacetate + H2O DMML also possesses significant oxaloacetate acetyl hydrolase activity Aspergillus niger oxalate + acetate
-
?

Subunits

Subunits Comment Organism
homotetramer 4 * 32000, SDS-PAGE Aspergillus niger
homotetramer 4 * 31986, mass spectrometry Aspergillus niger
homotetramer 4 * 32117, calculated from amino acid sequence Aspergillus niger

Synonyms

Synonyms Comment Organism
(2R,3S)-dimethylmalate lyase
-
Aspergillus niger
An07g08390
-
Aspergillus niger
DMML
-
Aspergillus niger

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.00001
-
oxaloacetate mutant enzyme Y44F, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
0.081
-
oxaloacetate mutant enzyme C124S, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
0.082
-
oxaloacetate mutant enzyme P240T, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
0.125
-
oxaloacetate mutant enzyme C124A, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
0.357
-
oxaloacetate mutant enzyme P240S, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
0.48
-
oxaloacetate wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
0.505
-
oxaloacetate wild type enzyme, in 0.1 M imidazole (pH 7.6 and 25°C) Aspergillus niger

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
-
Aspergillus niger

pH Range

pH Minimum pH Maximum Comment Organism
5 8
-
Aspergillus niger

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.0024
-
Phosphonopyruvate in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
0.0025
-
3,3-difluoroxaloacetate in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
1.6
-
oxalate in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger

General Information

General Information Comment Organism
metabolism DMML is a key enzyme in bacterial nicotinate catabolism Aspergillus niger

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
2
-
oxaloacetate wild type enzyme, in 0.1 M imidazole (pH 7.6 and 25°C) Aspergillus niger
2
-
oxaloacetate wild type enzyme, in 50 mM K+-HEPES (pH7.5 and 25°C) Aspergillus niger
70000
-
oxaloacetate mutant enzyme P240T, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
300000
-
oxaloacetate mutant enzyme P240S, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
900000
-
oxaloacetate mutant enzyme C124A, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger
3000000
-
oxaloacetate mutant enzyme C124S, in 50 mM K+-HEPES (pH 7.5 and 25°C) Aspergillus niger