Information on EC 4.1.3.32 - 2,3-Dimethylmalate lyase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
4.1.3.32
-
RECOMMENDED NAME
GeneOntology No.
2,3-Dimethylmalate lyase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(2R,3S)-2,3-dimethylmalate = propanoate + pyruvate
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Microbial metabolism in diverse environments
-
-
Nicotinate and nicotinamide metabolism
-
-
nicotinate degradation III
-
-
SYSTEMATIC NAME
IUBMB Comments
(2R,3S)-2,3-dimethylmalate pyruvate-lyase (propanoate-forming)
-
CAS REGISTRY NUMBER
COMMENTARY hide
73562-28-4
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
DMML is a key enzyme in bacterial nicotinate catabolism
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2R)-ethyl-(3S)-methylmalate
?
show the reaction diagram
-
-
-
?
(2R)-ethylmalate
?
show the reaction diagram
-
-
-
?
(2R)-methylmalate
?
show the reaction diagram
-
-
-
?
(2R)-propyl-(3S)-methylmalate
?
show the reaction diagram
-
-
-
?
(2R,3S)-2,3-dimethylmalate
propanoate + pyruvate
show the reaction diagram
-
-
-
?
(2R,3S)-2-methylisocitrate
?
show the reaction diagram
-
-
-
?
(2R,3S)-dimethylmalate
propanoate + pyruvate
show the reaction diagram
(2R,3S)-isocitrate
?
show the reaction diagram
-
-
-
?
(2R,3S)-methylisocitrate
?
show the reaction diagram
-
-
-
?
(2S)-methylmalate
?
show the reaction diagram
-
-
-
?
(2S,3R)-2-methylisocitrate
?
show the reaction diagram
-
-
-
?
(3S)-isopropylmalate
?
show the reaction diagram
-
-
-
?
(R)-malate
?
show the reaction diagram
-
-
-
?
(S)-malate
?
show the reaction diagram
-
-
-
?
2,3-Dimethylmalate
Propanoate + pyruvate
show the reaction diagram
3,3-difluoroxaloacetate
?
show the reaction diagram
-
-
-
?
3-butylmalate
?
show the reaction diagram
-
-
-
?
carboxyphosphoenolpyruvate
?
show the reaction diagram
-
-
-
?
oxaloacetate
?
show the reaction diagram
-
-
-
?
oxaloacetate
acetate + oxalate
show the reaction diagram
-
-
-
?
phosphonopyruvate
?
show the reaction diagram
-
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(2R,3S)-2,3-dimethylmalate
propanoate + pyruvate
show the reaction diagram
Q2L887
-
-
-
?
additional information
?
-
-
inducible enzyme
-
-
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2R,3S)-isocitrate
-
3,3-difluoroxaloacetate
; tight binding competitive inhibitor
carboxyphosphoenolpyruvate
-
cystamine
-
-
Disulfide
-
-
iodoacetamide
-
-
iodoacetate
Mg2+
-
above 10 mM; inhibits at high concentrations
oxalate
; weak binding competitive inhibitor
Phosphonopyruvate
-
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Mercaptans
-
activity is dependent on
-
thiols
-
dependent on
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.17
(2R)-ethyl-(3S)-methylmalate
; wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
12
(2R)-ethylmalate
; wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
2.2
(2R)-methylmalate
; wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
2.7
(2R)-propyl-(3S)-methylmalate
; wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
12
(2R,3S)-2-methylisocitrate
wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
0.036 - 7.4
(2R,3S)-dimethylmalate
12
(2R,3S)-methylisocitrate
-
12
(2S,3R)-2-methylisocitrate
; wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
0.66
2,3-dimethylmalate
-
-
0.027 - 1.22
oxaloacetate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
63
(2R)-ethyl-(3S)-methylmalate
Aspergillus niger
Q2L887
; wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
4.4
(2R)-ethylmalate
Aspergillus niger
Q2L887
; wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
2.64
(2R)-methylmalate
Aspergillus niger
Q2L887
; wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
0.79
(2R)-propyl-(3S)-methylmalate
Aspergillus niger
Q2L887
; wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
0.13
(2R,3S)-2-methylisocitrate
Aspergillus niger
Q2L887
wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
0.00001 - 19.2
(2R,3S)-dimethylmalate
0.00001
(2R,3S)-isocitrate
Aspergillus niger
Q2L887
smaller than 0.00001 s-1
0.13
(2R,3S)-methylisocitrate
Aspergillus niger
Q2L887
-
0.00001
(2S)-methylmalate
Aspergillus niger
Q2L887
smaller than 0.00001 s-1
0.13
(2S,3R)-2-methylisocitrate
Aspergillus niger
Q2L887
; wild type enzyme, at pH 7.5 and 25°C; wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
0.00001
(3S)-isopropylmalate
Aspergillus niger
Q2L887
smaller than 0.00001 s-1
0.00001
(R)-malate
Aspergillus niger
Q2L887
smaller than 0.00001 s-1
0.00001
(S)-malate
Aspergillus niger
Q2L887
smaller than 0.00001 s-1
0.00001
3,3-difluoroxaloacetate
Aspergillus niger
Q2L887
smaller than 0.00001 s-1
0.00001
3-butylmalate
Aspergillus niger
Q2L887
smaller than 0.00001 s-1
0.00001
carboxyphosphoenolpyruvate
Aspergillus niger
Q2L887
smaller than 0.00001 s-1
0.00001 - 0.505
oxaloacetate
0.00001
Phosphonopyruvate
Aspergillus niger
Q2L887
smaller than 0.00001 s-1
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
50
(2R)-ethyl-(3S)-methylmalate
Aspergillus niger
Q2L887
wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
11945
0.1
(2R)-ethylmalate
Aspergillus niger
Q2L887
wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
11944
1
(2R)-methylmalate
Aspergillus niger
Q2L887
wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
11943
0.3
(2R)-propyl-(3S)-methylmalate
Aspergillus niger
Q2L887
wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
11946
0.01
(2R,3S)-2-methylisocitrate
Aspergillus niger
Q2L887
wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
8544
0.005 - 2000000
(2R,3S)-dimethylmalate
1636
0.01
(2S,3R)-2-methylisocitrate
Aspergillus niger
Q2L887
wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)
11947
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5
(2E)-2-(phosphonooxy)but-2-enedioic acid
Ki above 5 mM
5
(2R,3S)-isocitrate
Ki above 5 mM; larger than 5 mM
5
(R)-malate
Ki above 5 mM; larger than 5 mM
5
(S)-malate
Ki above 5 mM; larger than 5 mM
0.0025 - 2.5
3,3-difluoroxaloacetate
5
carboxyphosphoenolpyruvate
larger than 5 mM
1.6
oxalate
; in 50 mM K+-HEPES (pH 7.5 and 25°C)
0.0024 - 2.4
Phosphonopyruvate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
; activity assay
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
activity assay
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.5 - 7.5
activity drops at higher pH
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
31400
-
4 * 31400, SDS-PAGE
31986
4 * 31986, mass spectrometry
31990
determined by mass spectrometry; mass spectrometry
32000
determined by SDS-PAGE; SDS-PAGE
32117
4 * 32117, calculated from amino acid sequence
32120
calculated from amino acid sequence; theoretical
110000
determined by gel-filtration chromatography; gel filtration
125000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
tetramer
x-ray crystallography
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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); in complex with Mg2+, hanging drop vapour diffusion method; the crystal structure of DMML in complex with Mg2+ and in complex with Mg2+ and a substrate analog, the gem-diol of 3,3-difluoro-oxaloacetate, is determined
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(NH4)2SO4 precipitation, Source Phe column chromatography, and Source 15Q FPLC column chromatography
-
by using a column chromatography-based protocol; Q-Sepharose column chromatography, ammonium sulfate precipitation, butyl Sepharose column chromatography, and phenyl Sepharose column chromatography
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21 cells
-
expressed in Escherichia coli; expressed in Escherichia coli BL21(DE3) cells; into the vector pGEM-T Easy and subsequently into pET3c for expression in Escherichia coli BL21DE3 cells
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C124A
reduced activity; site-directed mutant for testing the contributions made by key active-site residues; the mutant shows decreased kcat compared to the wild type enzyme
C124S
reduced activity; site-directed mutant for testing the contributions made by key active-site residues; the mutant shows decreased kcat compared to the wild type enzyme
D59A
reduced activity; site-directed mutant for testing the contributions made by key active-site residues; the mutant shows decreased kcat compared to the wild type enzyme
D59S
reduced activity; site-directed mutant for testing the contributions made by key active-site residues; the mutant shows decreased kcat compared to the wild type enzyme
P240S
reduced activity; site-directed mutant for testing the contributions made by key active-site residues; the mutant shows decreased kcat compared to the wild type enzyme
P240T
reduced activity; site-directed mutant for testing the contributions made by key active-site residues; the mutant shows decreased kcat compared to the wild type enzyme
Y44F
inactive; site-directed mutant for testing the contributions made by key active-site residues
Show AA Sequence (156 entries)
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