Information on EC 4.1.1.74 - Indolepyruvate decarboxylase

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

EC NUMBER
COMMENTARY hide
4.1.1.74
-
RECOMMENDED NAME
GeneOntology No.
Indolepyruvate decarboxylase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
3-(indol-3-yl)pyruvate = 2-(indol-3-yl)acetaldehyde + CO2
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
L-tryptophan degradation VII (via indole-3-pyruvate)
-
-
L-tryptophan degradation VIII (to tryptophol)
-
-
Metabolic pathways
-
-
methionine metabolism
-
-
tryptophan metabolism
-
-
Tryptophan metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
3-(indol-3-yl)pyruvate carboxy-lyase [(2-indol-3-yl)acetaldehyde-forming]
Thiamine diphosphate- and Mg2+-dependent. More specific than EC 4.1.1.1 pyruvate decarboxylase
CAS REGISTRY NUMBER
COMMENTARY hide
183213-32-3
-
9074-92-4
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Sp7
-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
no activity in Pseudomonas fluorescens
-
-
-
Manually annotated by BRENDA team
no activity in Pseudomonas fluorescens Psd
-
-
-
Manually annotated by BRENDA team
299R
-
-
Manually annotated by BRENDA team
299R
-
-
Manually annotated by BRENDA team
strain 7
-
-
Manually annotated by BRENDA team
strain 7
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
an ipdC-knockout mutant grown in the presence of tryptophan has decreased indole-3-acetic acid level (46% of wild type strain)
metabolism
IpdC id involved in indole-3-acetic acid biosynthesis
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(indol-3-yl)pyruvate
(indole-3-yl)acetaldehyde + CO2
show the reaction diagram
-
-
-
?
(indole-3-yl)pyruvate
(indole-3-yl)acetaldehyde + CO2
show the reaction diagram
-
-
-
-
?
2-oxoglutarate
?
show the reaction diagram
2-oxoisovalerate
?
show the reaction diagram
3-(indol-3-yl)pyruvate
(indole-3-yl)acetaldehyde + CO2
show the reaction diagram
-
-
-
?
3-(indol-3-yl)pyruvate
2-(indol-3-yl)acetaldehyde + CO2
show the reaction diagram
3-(Indol-3-yl)pyruvate
?
show the reaction diagram
3-(Indol-3-yl)pyruvate
Indole-3-acetaldehyde + CO2
show the reaction diagram
4-bromo-benzoylformic acid
4-bromobenzaldehyde + CO2
show the reaction diagram
-
-
-
?
4-chloro-benzoylformic acid
4-chlorobenzaldehyde + CO2
show the reaction diagram
-
-
-
?
4-ethyl-benzoylformic acid
4-ethylbenzaldehyde + CO2
show the reaction diagram
-
-
-
?
4-fluoro-benzoylformic acid
4-fluorobenzaldehyde + CO2
show the reaction diagram
-
-
-
?
4-hydroxyphenylpyruvate
(4-hydroxyphenyl)acetaldehyde + CO2
show the reaction diagram
-
-
-
-
4-methoxy-benzoylformic acid
4-methoxybenzaldehyde + CO2
show the reaction diagram
-
-
-
?
4-methyl-benzoylformic acid
4-methylbenzaldehyde + CO2
show the reaction diagram
-
-
-
?
4-nitro-benzoylformic acid
4-nitrobenzaldehyde + CO2
show the reaction diagram
-
-
-
?
benzaldehyde
?
show the reaction diagram
-
-
-
?
Benzoylformate
Benzaldehyde + CO2
show the reaction diagram
the enzyme shows the highest kcat value for benzoylformate
-
-
?
benzoylformic acid
benzaldehyde + CO2
show the reaction diagram
glyceraldehyde
?
show the reaction diagram
-
-
-
?
indole-3-acetaldehyde
?
show the reaction diagram
phenylacetaldehyde
?
show the reaction diagram
-
-
-
?
Pyruvate
Acetaldehyde + CO2
show the reaction diagram
Pyruvic acid
Acetaldehyde + CO2
show the reaction diagram
-
decarboxylation at 19% of the indole-3-acetic acid decarboxylation
-
-
-
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
(indol-3-yl)pyruvate
(indole-3-yl)acetaldehyde + CO2
show the reaction diagram
P51852
-
-
-
?
3-(indol-3-yl)pyruvate
(indole-3-yl)acetaldehyde + CO2
show the reaction diagram
P51852
-
-
-
?
3-(indol-3-yl)pyruvate
2-(indol-3-yl)acetaldehyde + CO2
show the reaction diagram
3-(Indol-3-yl)pyruvate
?
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
biotin
-
binds possibly to beta subunit
FMN
-
1.9 mol per mol of enzyme
thiamine diphosphate
additional information
-
no thiamine diphosphate
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe2+
-
8.7 mol per mol of enzyme
Mo2+
-
0.8 mol per mol of enzyme
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-oxoglutaric acid
-
-
3-(Indol-3-yl)pyruvate
substrate inhibition
3-phenylpyruvic acid
-
competitive against indole-3-acetic acid
4-hydroxyphenylpyruvate
substrate inhibition
benzoylformate
substrate inhibition
Pyruvic acid
-
-
SMIT568s10
knock-out strain, SMIT568s10 which shows a significant (50%) decrease in the levels of (indole-3-yl)acetic acid, (indole-3-yl)acetaldehyde and tryptophol compared to the wild type strain SM
-
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
indole-3-acetic acid
expression of ipdC is upregulated by indole-3-acetic acid, other auxins, and nutrient stress
L-phenylalanine
expression increases in response to
L-tryptophan
L-tyrosine
expression increases in response to
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0045 - 0.032
3-(Indol-3-yl)pyruvate
0.019
4-bromo-benzoylformic acid
-
pH 6.5, 30C
0.048
4-chloro-benzoylformic acid
-
pH 6.5, 30C
0.111
4-ethyl-benzoylformic acid
-
pH 6.5, 30C
0.62
4-fluoro-benzoylformic acid
-
pH 6.5, 30C
5.86
4-hydroxyphenylpyruvate
at pH 6.5, temperature not specified in the publication
1.05
4-methoxy-benzoylformic acid
-
pH 6.5, 30C
0.127
4-methyl-benzoylformic acid
-
pH 6.5, 30C
0.005
4-nitro-benzoylformic acid
-
pH 6.5, 30C
0.395
benzaldehyde
-
70C, pH 8.0
7.3
benzoylformate
at pH 6.5, temperature not specified in the publication
0.024 - 2.72
benzoylformic acid
0.042
glyceraldehyde
-
70C, pH 8.0
0.009
Indole-3-acetaldehyde
-
70C, pH 8.0
0.02 - 0.788
Indole-3-pyruvate
0.105
phenylacetaldehyde
-
70C, pH 8.0
1.66
phenylpyruvate
-
70C, pH 8.0
0.63 - 43.3
pyruvate
2.5
Pyruvic acid
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.04 - 2.05
3-(Indol-3-yl)pyruvate
1.65
4-hydroxyphenylpyruvate
Methylobacterium extorquens
C5ARG4
at pH 6.5, temperature not specified in the publication
31.4
benzoylformate
Methylobacterium extorquens
C5ARG4
at pH 6.5, temperature not specified in the publication
0.01 - 11.6
benzoylformic acid
0.016 - 2.06
pyruvate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
25.6
3-(Indol-3-yl)pyruvate
Methylobacterium extorquens
C5ARG4
at pH 6.5, temperature not specified in the publication
3503
0.28
4-hydroxyphenylpyruvate
Methylobacterium extorquens
C5ARG4
at pH 6.5, temperature not specified in the publication
423
4.3
benzoylformate
Methylobacterium extorquens
C5ARG4
at pH 6.5, temperature not specified in the publication
613
0.021
pyruvate
Methylobacterium extorquens
C5ARG4
at pH 6.5, temperature not specified in the publication
31
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.73
3-(Indol-3-yl)pyruvate
at pH 6.5, temperature not specified in the publication
22.11
4-hydroxyphenylpyruvate
at pH 6.5, temperature not specified in the publication
3.4
benzoylformate
at pH 6.5, temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.102
strain SMIT568s10, product: (indole-3-yl)ethanol, substrate: -Trp
0.217
strain SMIT568s10, product: (indole-3-yl)acetaldehyde, substrate: -Trp
0.268
strain SM, product: (indole-3-yl)ethanol, substrate: -Trp
0.615
strain SM, product: (indole-3-yl)acetaldehyde , substrate: -Trp
0.626
strain SMIT568s10, product: (indole-3-yl)ethanol, substrate: +Trp
1.006
strain SMIT568s10, product: (indole-3-yl)acetaldehyde, substrate: +Trp
1.252
strain SM, product: (indole-3-yl)ethanol, substrate: +Trp
2.3
strain SM, product: (indole-3-yl)acetaldehyde , substrate: +Trp
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.4 - 6.6
-
-
8
-
70% loss of activity at pH 7.0, 15% loss of activity at pH 9
8.2
external pH influences ipdC expression as maximum expression is observed at the alkaline pH of 8.2 (69% increase) while highly acidic pH decreases the expression level. At pH 4.2, expression is ca. 32% of that observed at pH 7.0
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
temperatures on either side of the growth optimum (30C) are found to alter ipdC expression significantly. At 25C a 48% increase and at 37C an 86% increase are noted
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
57500
tyrR insertional mutant
63380
-
SDS-PAGE, purified, corresponding closely to the expected molecular mass
240000
-
gel filtration
245000
280000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
homotetramer
4 * 60000, SDS-PAGE
tetramer
additional information
-
at pH-values between pH 5.6 and 6.0 the tetrameric form dominates, at pH values above 8.0, the monomeric form is present
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
expression of ipdC is upregulated by an increase in pH
692100
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
24 h, in presence of 1 mM thiamine diphosphate and 5 mM MgCl2, stable
50
-
30 min, in presence of 1 mM thiamine diphosphate and 5 mM MgCl2, stable
70
-
30 min, pH 7.0, almost stable
90
-
30 min, 22% inactivation
100
-
30 min, 97% inactivation
additional information
expression of ipdC is upregulated by temperature
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate stabilizes
-
less stable at a high potassium phosphate concentration
-
slightly stabilized in presence of 5 mM MgCl2
-
stabilized by addition of 1 mM thiamine diphosphate
-
thiamine diphosphate stabilizes
-
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ethanol
-
rather stable in ethanol
Ethyl acetate
-
rather stable in ethyl acetate
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, 20% (v/v) glycerol with addition of thiamine diphosphate/Mg2+, six months, the enzyme remains quite stable
quite stable at 40C without further additions
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Ni-NTA column chromatography, gel filtration
recombinant enzyme from Escherichia coli
-
recombinant enzyme from Escherichia coli cells
-
recombinant protein, purified to homogeneity using affinity chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloned in Escherichia coli DH5alpha, recombinant protein expressed in Escherichia coli BL21 (DE3) as a glutathione S-transferase (GST)-fusion protein
-
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli DH5alpha cells
-
expressed in Pseudomonas fluorescens strain Psd
-
heterologous overexpression of a functional iaaC gene from strain Sp245 in strain SM confirms its role in controlling IAA biosynthesis and lowering ipdC expression which may be effected by dissociating indole-3-acetic acid-transcriptional regulator interactions in the 5'region
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D29E
-
significant decrease in Km-values
E468D
-
slight decrease in Km-values
E52D
-
decrease in Km-value for 3-(indol-3-yl)pyruvate and pyruvate, increase in Km-value for benzoylformic acid
H115K
-
slight increase in Km-value for 3-(indol-3-yl)pyruvate and pyruvate, decrease in Km-value for benzoylformic acid
Q383T
-
decrease in Km-value for pyruvate
tyrR insertional mutant
activity of tyrR in Enterobacter cloacae UW5 is abolished by insertion of a tetracycline resistance cassette into the coding sequence, creating Enterobacter cloacae J35
additional information
ipdC gene knock-out, strain SMIT568s10 which shows a significant (50%) decrease in the levels of indole-3-acetic acid, indole-3-acetaldehyde and tryptophol compared to the wild type strain SM. Reduction in the plant growth promoting response of strain SMIT568s10 is observed in terms of root length and lateral root proliferation as well as the total dry weight of the treated plants
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