Information on EC 4.1.1.3 - oxaloacetate decarboxylase

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

EC NUMBER
COMMENTARY hide
4.1.1.3
-
RECOMMENDED NAME
GeneOntology No.
oxaloacetate decarboxylase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
oxaloacetate = pyruvate + CO2
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
carboxylation
-
-
-
-
decarboxylation
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
methylgallate degradation
-
-
protocatechuate degradation I (meta-cleavage pathway)
-
-
syringate degradation
-
-
gluconeogenesis
-
-
isoleucine metabolism
-
-
Pyruvate metabolism
-
-
Metabolic pathways
-
-
SYSTEMATIC NAME
IUBMB Comments
oxaloacetate carboxy-lyase (pyruvate-forming)
The enzyme from Klebsiella aerogenes is a biotinyl protein and also decarboxylates glutaconyl-CoA and methylmalonyl-CoA. The process is accompanied by the extrusion of two sodium ions from cells. Some animal enzymes require Mn2+.
CAS REGISTRY NUMBER
COMMENTARY hide
9024-98-0
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
guinea pig
-
-
Manually annotated by BRENDA team
genes oadA, oadB, oadC, and oadD
-
-
Manually annotated by BRENDA team
sunflower
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
CRL264
-
-
Manually annotated by BRENDA team
formerly Micrococcus lysodeiktikus
-
-
Manually annotated by BRENDA team
rabbit
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
rat
-
-
Manually annotated by BRENDA team
pig
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3-methyloxaloacetate
2-oxobutanoate + CO2
show the reaction diagram
-
-
-
?
oxaloacetate
?
show the reaction diagram
Oxaloacetate
Pyruvate + CO2
show the reaction diagram
Pyruvate + CO2
Oxaloacetate
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
oxaloacetate
?
show the reaction diagram
Oxaloacetate
Pyruvate + CO2
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
biotin
NADP+
additional information
no nicotinamide cofactors required
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Cd2+
-
activates
Li+
-
Km: 25 mM
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-oxoglutarate
-
2 mM inhibitor in presence of 10 mM Mn2+, 11% inhibition
2-Oxomalonate
3,3-difluoroxaloacetate
-
5,5'-dithiobis(2-nitrobenzoate)
-
-
acetate
-
competitive for oxaloacetate, Ki: 12 mM
acetic acid
-
noncompetitive
alpha-ketovalerate
-
Avidin
-
azide
-
2 mM, 20% inhibition
Ca2+
-
2 mM inhibitor in presence of 1 mM Mn2+, 30% inhibition
citrate
coenzyme A
diethylstilbestrol
-
95% inhibition at 50 mM
fumarate
-
2 mM inhibitor in presence of 10 mM Mn2+, 21% inhibition
Glycine-NaOH
-
-
glyoxylate
hydrogencarbonate
-
-
KSCN
-
95% inhibition at 50 mM, completely reversible
L-malate
malate
malic acid
-
competitive
malonate
N-ethylmaleimide
Ni2+
-
2 mM inhibitor in presence of 1 mM Mn2+, 40% inhibition
oxalate
oxalic acid
-
competitive
oxomalonate
p-chloromercuribenzoate
p-hydroxymercuribenzoate
phosphoenolpyruvate
Phosphonopyruvate
-
pyruvate
succinate
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
citrate
-
expression is induced by citrate
EDTA
-
activating below 5 mM
NaCl
-
highest activity with 1-1.4 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.63
3-methyloxaloacetate
wild type enzyme, in 0.2 mM NADH, 5 mM MgCl2 and 50 mM K+HEPES (pH 7.5), at 25°C
0.0003 - 4.3
oxaloacetate
3.3
pyruvate
-
-
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
250
3-methyloxaloacetate
in 0.2 mM NADH, 5 mM MgCl2 and 50 mM K+HEPES (pH 7.5), at 25°C
3.5 - 7500
oxaloacetate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
22.3
oxaloacetate
calculated value at pH 4.5, temperature not specified in the publication
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.06
2-Oxomalonate
-
-
0.45
3,3-difluoroxaloacetate
-
18.4
acetic acid
-
pH 8.0, 25°C
1.09
Acetopyruvate
-
1.5 - 5.1
ADP
6.7
alpha-ketovalerate
-
1.5
ATP
-
-
2.4
coenzyme A
-
-
0.04
glyoxylate
-
-
2.2
hydrogencarbonate
-
pH 8.0, 25°C
21.4
malic acid
-
pH 8.0, 25°C
2.5
Mn2+
-
pH 8.0, 25°C
198
NaCl
-
wild type enzyme, pH 6.9
0.0035 - 0.043
oxalate
0.6
oxalic acid
-
pH 8.0, 25°C
0.5
p-chloromercuribenzoate
-
-
7.8 - 28
phosphoenolpyruvate
3
Phosphonopyruvate
-
1.3 - 7.2
pyruvate
additional information
additional information
-
Ki-values given for inhibition with NaCl for all mutant enzymes at 3-4 different pH
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.54
-
-
3.15
-
purified enzyme, pH 7.1
9
-
alpha-chain, independent of Na+
45
-
wild type enzyme
319
-
pH 8.0, 25°C
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5
-
cytoplasmic enzyme
5.5
-
Q192L and Y209A mutants
6
-
enzyme assay at
6.25 - 6.75
-
wild type enzyme
6.5 - 7.5
6.5 - 7
-
wild type enzyme
6.5 - 7.5
7.1
-
-
8.5
-
pH-optima above 8.5 found for N373L, R389A, R389L mutant enzymes
9.2
-
R389A mutant
9.5
-
mitochondrial enzyme
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3.5 - 5.5
-
pH 3.5: about 55% of maximal activity, pH 5.5: about 40% of maximal activity
6 - 8
-
-
6 - 8.5
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-
7 - 10
-
-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
-
enzyme assay at
25
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enzyme assay at
37
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enzyme assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
58
-
no activity above
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10600
-
1 * 63800 + 1 * 34500 + 1 * 10600, alpha,beta,gamma, SDS-PAGE
29000
-
2 * 29000, gel filtration
31700
-
4 * 31700, SDS-PAGE
32000
-
monomer, SDS-PAGE
34500
-
1 * 63800 + 1 * 34500 + 1 * 10600, alpha,beta,gamma, SDS-PAGE
49000
-
2 * 49000, SDS-PAGE
51000
-
2 * 51000, gel filtration
58000
-
gel filtration
62100
-
native enzyme, gel filtration
63000
-
gel filtration
63600
-
alpha-subunit, calculated from amino acid sequence
63800
-
1 * 63800 + 1 * 34500 + 1 * 10600, alpha,beta,gamma, SDS-PAGE
65000
-
1 * 65000 + 1 * 34000 + 1 * 12000 alpha,beta,gamma, SDS-PAGE, subunits carry different functions
80000
-
gel filtration
98300
-
static light scattering
102000
-
gel filtration
105000
-
gel filtration
118000
-
gel filtration
530000
-
the most prominent band at 530 kDa is likely composed of a tetrameric Oad-alpha/gamma plus a dimeric (or tetrameric) Oad-beta subunit, SDS-PAGE
570000
oxaloacetate decarboxylase OAD-2, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterotrimer
homodimer
monomer
-
1 * 63000, SDS-PAGE
tetramer
trimer
additional information
-
the alpha-subunit binds the gamma-subunit with a distinct association domain which is flanked on both sides with proline- and alanine-rich linker peptides
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 0.2 M MgCl2, 0.1 M Bis-Tris pH 6.0, 25% (w/v) polyethylene glycol 3350
-
hanging drop vapour diffusion method, aliquots of 10 mg/ml protein in 5 mM MgCl2, 5 mM phosphonopyruvate and 10 mM NaHEPES (pH 7.0) mixed with equal volumes of reservoir solution containing 12% polyethylene glycol 20000 and 0.1 M MES (pH 6.0)
sitting drop vapour diffusion method using 0.1 M sodium cacodylate (pH 6.5), 0.2 M (NH4)2SO4, 5% (v/v) glycerol and 25% (w/v) PEG 8000
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3
-
-
4273
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
-
only if protected by oxalate
55
-
up to
85
-
half life for inacivation, 5 h
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
buffer-dependent, mercaptoethanol stabilises
-
very instable, protease-sensitive, 50% loss of activity after 4 min at 4°C
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, potassium phosphate buffer, pH 7, 50% glycerol, 2 month
-
25°C, 50 mM triethanolamine/HCl, pH 7.0, 5 days, almost complete inactivation, presence of 1 mM Mn2+ and 50% v/v glycerol stabilize
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4°C, glycerol, 2 months
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4°C, phosphate buffer or arsenate buffer, pH 7, with mercaptoethanol, N2-atmosphere, 2 months
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4°C, Tris-HCl buffer, pH 7.5, 2 month, 40% loss of activity
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frozen, Tris-HCl buffer, pH 7.5, 1 month, 25% loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
alpha- and beta-chain
-
alpha-chain
-
ammonium sulfate precipitation, HiPrep column chromatography, Mono Q column chromatography, and Superdex-200 gel filtration
-
avidin-Sepharose column chromatography
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DEAE-cellulose column chromatography, phenyl-Sepharose columnn chromatography, and butyl-Sepharose column chromatography
enzyme from Vibrio cholerae and heterologously expressed enzyme
Ni-NTA column chromatography and Superdex G-200 gel filtration
-
Ni2+-bounded affinity column chromatography
Ni2+-NTA-agarose column chromatography
-
recombinant
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recombinant enzyme from Escherichia coli
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recombinant protein from Escherichia coli
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recombinnat maltose-binding protein fusion protein OadH from Escherichia coli by amylase affinity chromatography, recombinant His-tagged subunits from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
all subunits, expressed in Escherichia coli, alpha-subunit strongly overexpressed from pT7-7 plasmid
-
alpha-subunit, expressed in Escherichia coli
-
expressed in Escherichia coli
-
expressed in Escherichia coli BL21 (DE3) cells
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli C43 (DE3) cells
-
expressed in Escherichia coli C43(DE3) cells
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expressed in Escherichia coli CC118
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expressed in Escherichia coli DH5alpha
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expressed in Escherichia coli DH5alpha/pSK-GAB
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expressed in Escherichia coli Rosetta (C43) cells
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expressed in Escherichia coli strain C43(DE3)
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expression in Escherichia coli
-
expression in Escherichia coli M15
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expression in Escherichia coli, expression of mutant enzymes and domains of the alpha subunit
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expression in Escherichia coli; expression in Escherichia coli
expression of gene oadH as maltose-binding protein fusion protein in Escherichia coli, genes oadA-oadD, expression of recombinant His-tagged subunits in Escherichia coli strain BL21(DE3)
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when subunit alpha-2 of oxaloacetate decarboxylase OAD-2 and the C-terminal domain of gamma-2 are synthesized together in Escherichia coli they form a complex that is stable at neutral pH and dissociates at pH-values below 5.0
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Y235A
-
site-directed mutagenesis
Y235F
-
site-directed mutagenesis
Y235S
-
site-directed mutagenesis
A383C
-
beta subunit, very low activity, low activity after modification with 2-aminoethyl methanethiosulfonate
C291E
-
beta subunit, unstable in the absence of Na+, dissociates into an alpha-gamma subcomplex and the beta subunit
C87A
-
slightly increased activity
C87A/A194C
-
no effect on activity
C87A/I198C
-
no effect on activity
C87A/L178C
-
about 50% of activity
C87A/L7C
-
no activity
C87A/P191C
-
no activity
C87A/P205C
-
no effect on activity; only traces of activity
C87A/S187C
-
no effect on activity
C87A/V129C
-
strongly increased activity
C87A/Y182C
-
slightly increased activity
D203N
-
beta subunit, complete loss of activity
D62A
-
gamma subunit, Zn2+ content decreased to 35% of the wild type enzyme, roughly 30% of activity
D63A
-
gamma subunit, almost no effect on activity
DELTAH76-P83
-
gamma subunit, unable to associate to the alpha subunit, no activity
DELTAH78-P83
-
gamma subunit, unable to associate to the alpha subunit, no activity
DELTAH82-P83
-
gamma subunit, Zn2+ content decreased to 5% of the wild type enzyme, very low activity
G337A
-
beta subunit, complete loss of activity
G377A
-
beta subunit, complete loss of activity
G377C
-
beta subunit, no activity even after modification with 2-aminoethyl methanethiosulfonate
G380A
-
beta subunit, about 30% of activity
G380C
-
beta subunit, very low activity, low activity after modification with 2-aminoethyl methanethiosulfonate
H76A
-
gamma subunit, almost no effect on activity
H77A
-
gamma subunit, Zn2+ content decreased to 10% of the wild type enzyme, very low activity
H78A
-
gamma subunit, binding to alpha subunit is lost; gamma subunit, unable to associate to the alpha subunit, no activity
N373D
-
beta subunit, no protection against tryptic digestion by Na+
N392L
-
beta subunit, about 70% of activity
Q192L
-
beta subunit, lower pH optimum than wild type enzyme
R389C
-
beta subunit, increased pH-optimum, reduced activity, activity and pH-optimum can be restored to wild type value by modification with 2-aminoethyl methanethiosulfonate
R389K
-
beta subunit, about 80% of activity, significantly decreased Na+ binding
R389L
-
beta subunit, about 10% of activity, significantly decreased Na+ binding
S382E
-
beta subunit, complete loss of activity
S382N
-
beta subunit, complete loss of activity
S382Q
-
beta subunit, complete loss of activity
Y209A
-
beta subunit, lower pH optimum than wild type enzyme
Y229F
-
beta subunit, completely inactive
H235A
the kcat value for catalysis of oxaloacetate decarboxylation is less than an order of magnitude smaller compared to the wild type enzyme
H235Q
the kcat value for catalysis of oxaloacetate decarboxylation is less than an order of magnitude smaller compared to the wild type enzyme
Y212F
25fold reduction of the Km value compared to the wild type enzyme
C148A
-
74% activity of the wild type enzyme
C148S
-
54% activity of the wild type enzyme
D17A
-
inactive
H207I
-
inactive
H209I
-
inactive
K178I
-
inactive
K178R
-
inactive
M180I
-
16% activity of the wild type enzyme
Q20L
-
inactive
R16I
-
inactive
additional information
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
heterologously expressed oxaloacetate decarboxylase OAD-2
reconstition of isolated alpha-chains and bacterial membranes containing beta- and gamma-chains
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
-
optimization of oxaloacetate may increase lysine productivity of commercially used strains
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