Information on EC 4.1.1.71 - 2-oxoglutarate decarboxylase

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

EC NUMBER
COMMENTARY
4.1.1.71
-
RECOMMENDED NAME
GeneOntology No.
2-oxoglutarate decarboxylase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-oxoglutarate = succinate semialdehyde + CO2
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
decarboxylation
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
TCA cycle IV (2-oxoglutarate decarboxylase)
-
-
SYSTEMATIC NAME
IUBMB Comments
2-oxoglutarate carboxy-lyase (succinate-semialdehyde-forming)
Requires thiamine diphosphate. Highly specific.
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ALKBH4
-
-
alpha-ketoglutarate decarboxylase
-
-
-
-
alpha-ketoglutarate decarboxylase
A0R2B1
-
alpha-ketoglutarate decarboxylase
A0R3B1
-
alpha-ketoglutarate decarboxylase
Mycobacterium smegmatis MC2 155
A0R2B1
-
-
alpha-ketoglutarate decarboxylase
-
-
alpha-ketoglutarate decarboxylase
-
-
-
alpha-ketoglutaric decarboxylase
-
-
-
-
decarboxylase, oxoglutarate
-
-
-
-
Fe(II)/2OG-dependent decarboxylase
-
-
KDC
-
-
-
-
Kgd
Mycobacterium smegmatis MC2 155
A0R2B1
-
-
oxoglutarate decarboxylase
-
-
-
-
pre-2-oxoglutarate decarboxylase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
37205-42-8
-
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
lacking a 2-oxoglutarate dehydrogenase complex (EC 1.2.4.2 + EC 2.3.1.61 + EC 1.8.1.4)
-
-
Manually annotated by BRENDA team
strain SM-ZK
-
-
Manually annotated by BRENDA team
Euglena gracilis SM-ZK
strain SM-ZK
-
-
Manually annotated by BRENDA team
Mycobacterium smegmatis MC2 155
-
UniProt
Manually annotated by BRENDA team
Oenococcus oeni B 211
B 211
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
A0R2B1
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
A0R3B1
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
-
highly specific
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
-
highly specific
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
Mycobacterium smegmatis MC2 155
A0R2B1
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
Oenococcus oeni B 211
-
-
-
-
?
oxaloacetate
?
show the reaction diagram
Oenococcus oeni, Oenococcus oeni B 211
-
28% of the activity with 2-oxoglutarate
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
Euglena gracilis SM-ZK
-
-
-
?
additional information
?
-
-
the enzyme has a physiologically important role coupling with succinate-semialdehyde dehydrogenase in the tricarboxylic acid cycle
-
-
-
additional information
?
-
-
the 2-oxoglutarate dehydrogenase complex: 2-oxoglutarate decarboxylase and lipoamide dehydrogenase is a rate-limiting mitochondrial enzyme of the tricarboxylic acid cycle
-
-
-
additional information
?
-
-
enzyme has physiological function in the assimilation of L-glutamate
-
-
-
additional information
?
-
-
enzyme and GabD1 or GabD2 form an alternative pathway from 2-oxoglutarate to succinate, no substrate: pyruvate
-
-
-
additional information
?
-
Euglena gracilis SM-ZK
-
enzyme has physiological function in the assimilation of L-glutamate
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
A0R2B1
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
A0R3B1
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
Mycobacterium smegmatis MC2 155
A0R2B1
-
-
-
?
2-oxoglutarate
succinate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
additional information
?
-
-
the enzyme has a physiologically important role coupling with succinate-semialdehyde dehydrogenase in the tricarboxylic acid cycle
-
-
-
additional information
?
-
-
the 2-oxoglutarate dehydrogenase complex: 2-oxoglutarate decarboxylase and lipoamide dehydrogenase is a rate-limiting mitochondrial enzyme of the tricarboxylic acid cycle
-
-
-
additional information
?
-
-
enzyme has physiological function in the assimilation of L-glutamate
-
-
-
additional information
?
-
-
enzyme and GabD1 or GabD2 form an alternative pathway from 2-oxoglutarate to succinate
-
-
-
additional information
?
-
Euglena gracilis SM-ZK
-
enzyme has physiological function in the assimilation of L-glutamate
-
-
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NADP+
-
stimulates
NADPH
-
stimulates
thiamine diphosphate
-
Km: 0.056 mM; required
thiamine diphosphate
-
0.03 mM; required
thiamine diphosphate
-
Km-value 0.019 mM
thiamine diphosphate
A0R3B1
-
ATP
-
slight stimulation
additional information
-
no cofactor: coenzyme A, NAD+, NADP+
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
-
can partially replace Mg2+ in activation
Ca2+
-
no effect
Co2+
-
can partially replace Mg2+ in activation
Co2+
-
no effect
Fe2+
-
dependent on
Mg2+
-
strictly required, Km-value 0.196 mM
MgCl2
-
required
MgCl2
-
Km: 0.093 mM; stimulates
Mn2+
-
stimulates
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1,10-phenanthroline
-
-
1,10-phenanthroline
-
-
2,4-Dinitrophenol
-
-
2-oxoglutarate
-
above 2 mM substrate inhibition
Isocitrate
-
-
NH4Cl
-
preferential sensitivity of enzyme to NH4Cl in vitro in nonsynaptic mitochondria and hyperammonemic conditions in vivo in synaptic mitochondria
Succinic semialdehyde
-
-
m-chlorophenylhydrazone
-
-
additional information
-
not: NaN3
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-mercaptoethanol
-
stimulates
2-mercaptoethanol
-
stimulates
2-oxoglutarate
-
-
citrate
-
-
DL-malate
-
-
DTT
-
stimulates
DTT
-
stimulates
fumarate
-
-
L-alanine
-
-
L-aspartate
-
-
L-glutamate
-
activation is abolished by the simultaneous addition of cycloheximide
L-lactate
-
-
Propionate
-
-
pyruvate
-
-
succinate
-
-
thiamine
-
the activation of enzyme by thiamine is caused by two mechanism, the increase in the apoenzyme of enzyme by thiamine added exogenously is attributable to the conversion from the premature form to the mature form of enzyme during import into the mitochondria from cytosol, 1,10-phenanthroline, 2,4-dinitrophenol, carbonyl cyanide m-chlorophenylhydrazone inhibit activation
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.33
2-oxoglutarate
-
pH 7.0, 30C
0.33
2-oxoglutarate
-
pH 7.0
0.48
2-oxoglutarate
-
22C, pH 7.0
1
2-oxoglutarate
-
pH 5.3, 30C
additional information
additional information
-
comparison of the effect of NH4Cl in vitro, hepatic encephalopathy, and hyperammonemia on KM in synaptic and nonsynaptic brain mitochondria
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4 - 6.5
-
active in the range
6 - 9
-
pH 6.0: 65% of activity maximum, pH 9.0: 55% of activity maximum
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
35 - 40
-
35-40C: activity maximum, maximum activity is maintained up to 60C
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.2
-
isoelectric focusing
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
synaptic and nonsynaptic
Manually annotated by BRENDA team
additional information
-
not: cytosol, microsomes
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
70000
-
PAGE
648366
250000
-
gel filtration
648365
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
-
x-ray crystallography
homodimer
A0R2B1
x-ray crystallography
homodimer
Mycobacterium smegmatis MC2 155, Mycobacterium tuberculosis H37Rv
-
x-ray crystallography
-
monomer
-
1 * 65000, SDS-PAGE
monomer
Oenococcus oeni B 211
-
1 * 65000, SDS-PAGE
-
tetramer
-
4 * 62000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 39-46.5% (w/v) 2-methyl-2,4-pentanediol, 100 mM HEPES (pH 7.0), 200 mM NaCl
A0R2B1
hanging drop vapor diffusion method, using 52-59% (w/v) 2-methyl-2,4-pentanediol and 22-25 mM sodium acetate
A0R3B1
hanging drop vapor diffusion method, using 39-46.5% (w/v) 2-methyl-2,4-pentanediol, 100 mM HEPES (pH 7.0), 200 mM NaCl
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.2 - 8.5
-
62C, 10 min, stable
648365
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
57.5
-
10 min, stable up to
648365
60
-
pH 5.3, 30 min, 10% loss of activity
648366
62
-
pH 6.2-8.5, 10 min, stable
648365
67
-
10 min, complete loss of activity
648365
70
-
complete loss of activity at 70C
648364
70
-
pH 5.3, 5 min, 90% loss of activity
648366
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
the isolated proteins (ALKBH4 and mutants), even when kept in iced-cooled solutions (4C), aggregate and then precipitate at concentrations higher than 0.5 mM. The process is accelerated greatly when an excess (e.g. 5fold) of dithionite is added to the solution when anaerobic Fe(II)-reconstitution procedures are carried out
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4C or -20C, 24 h, 95% or 25% loss of activity, respectively
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
glutathione-Sepharose column chromatography, gel filtration
-
HisTrap column chromatography and Ni-NTA agarose column chromatography
A0R2B1
HisTrap column chromatography and Ni-NTA agarose column chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21-CodonPlus(DE3)-RIPL cells
-
expressed in Escherichia coli
A0R3B1
expressed in Escherichia coli BL21(DE3)pLysS cells
A0R2B1
expressed in Escherichia coli BL21(DE3)pLysS cells
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C15A/C17A
-
the mutant displays a decarboxylation activity similar to that of the wild type enzyme
H169A/D171A
-
the mutant is devoid of the ability to perform 2-oxoglutarate turnover