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Information on EC 1.2.4.2 - oxoglutarate dehydrogenase (succinyl-transferring) and Organism(s) Escherichia coli and UniProt Accession P0AFG3
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1.2.4.2 oxoglutarate dehydrogenase (succinyl-transferring)IUBMB Comments
Contains thiamine diphosphate. It is a component of the multienzyme 2-oxoglutarate dehydrogenase complex, EC 1.2.1.105, in which multiple copies of it are bound to a core of molecules of EC 2.3.1.61, dihydrolipoyllysine-residue succinyltransferase, which also binds multiple copies of EC 1.8.1.4, dihydrolipoyl dehydrogenase. It does not act on free lipoamide or lipoyllysine, but only on the lipoyllysine residue in EC 2.3.1.61.
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Word Map
- 1.2.4.2
- succinate
-
tricarboxylic
- malate
- isocitrate
- tca
- thiamin
- citrate
- dehydrogenases
-
krebs
- dihydrolipoamide
-
citric
- neurodegenerative
-
lipoylation
- alzheimer
-
lipoic
- lipoamide
- aconitase
-
branched-chain
- transketolase
-
succinylation
-
intramitochondrial
- succinyl-coa
- oxaloacetate
- hexokinase
- acidosis
- glyoxylate
- glutamicum
- fumarase
- encephalopathy
-
antimitochondrial
- glutaminase
-
pigeon
- alpha-ketoacids
-
aciduria
-
thiamine-dependent
-
thiamine-deficient
-
ca2+-sensitive
- 2-oxo-acid
-
anaplerotic
- 6-phosphofructokinase
- wernicke
-
ketoacids
- dihydrolipoate
- thiokinase
-
1.2.4.1
-
diphosphate-dependent
-
nadh-linked
-
malate-aspartate
- pdc-e2
- industry
- synthesis
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
Synonyms
alpha-ketoglutarate dehydrogenase, 2-oxoglutarate dehydrogenase, kgdhc, alpha-ketoglutarate dehydrogenase complex, 2-oxoglutarate dehydrogenase complex, oxoglutarate dehydrogenase, kgdh, dhtkd1, ogdhl, ogdhc, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex
-
2-ketoglutarate dehydrogenase
-
-
-
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2-OGDH
-
-
-
-
2-oxoglutarate decarboxylase
-
part of the 2-oxoglutarate dehydrogenase complex
2-oxoglutarate dehydrogenase
2-oxoglutarate:lipoate oxidoreductase
-
-
-
-
AKGDH
-
-
-
-
alpha-ketoglutarate dehydrogenase
-
-
-
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alpha-ketoglutaric acid dehydrogenase
-
-
-
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alpha-ketoglutaric dehydrogenase
-
-
-
-
alpha-KGD
-
-
-
-
alpha-oxoglutarate dehydrogenase
-
-
-
-
dehydrogenase, oxoglutarate
-
-
-
-
E1o
ketoglutaric dehydrogenase
-
-
-
-
OGDC
-
-
-
-
oxoglutarate decarboxylase
-
-
-
-
oxoglutarate dehydrogenase
-
-
-
-
2-oxoglutarate dehydrogenase
-
-
-
-
E1o
-
2-oxoglutarate dehydrogenase subunit of the 2-oxoglutarate dehydrogenase complex
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2
2-oxoglutarate dehydrogenase complex consists of 3 enzymes: E1 (alpha-ketoglutarate dehydrogenase, EC 1.2.4.2), E2 (dihydrolipoyl transsuccinylase, EC 2.3.1.61), E3 (dihydrolipoyl dehydrogenase, EC 1.8.1.4)
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2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2
the enzyme complex catalyzes the reaction : 2-oxoglutarate + CoA + NAD+--> succinyl-CoA + CO2 + NADH, the following partial reactions are catalyzed: 1. HOOC(CH2)2COCOOH + (thiamine diphosphate)-E1--> (HOOC(CH2)2 CHOH-thiamine-diphosphate)-E1 + CO2, 2. (HOOC(CH2)2CH OH-thiamine-diphosphate)-E1 + (LipS2)-E2--> (HOOC(CH)2 CO-(SLipSH))-E2 + (thiamine-diphosphate)-E1, 3. (HOOC(CH2)2CO-(SLipSH))-E2 + HSCoA--> (Lip(SH)2)-E2 + HOOC(CH2)2CO-SCoA, 4. (Lip(SH)2)-E2 + E3-FAD--> (LipS2)-E2 + reduced E3-FAD, 5. reduced E3-FAD + NAD+--> E3-FAD + NADH
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
-
-
-
-
oxidation
-
-
-
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reduction
-
-
-
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oxidative decarboxylation
-
-
-
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PATHWAY SOURCE
PATHWAYS
KEGG
-
-
SYSTEMATIC NAME
IUBMB Comments
2-oxoglutarate:[dihydrolipoyllysine-residue succinyltransferase]-lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-succinylating)
Contains thiamine diphosphate. It is a component of the multienzyme 2-oxoglutarate dehydrogenase complex, EC 1.2.1.105, in which multiple copies of it are bound to a core of molecules of EC 2.3.1.61, dihydrolipoyllysine-residue succinyltransferase, which also binds multiple copies of EC 1.8.1.4, dihydrolipoyl dehydrogenase. It does not act on free lipoamide or lipoyllysine, but only on the lipoyllysine residue in EC 2.3.1.61.
CAS REGISTRY NUMBER
COMMENTARY
9031-02-1
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine
[dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2
-
-
-
?
2-oxo-5-hexenoic acid + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine
[dihydrolipoyllysine-residue succinyltransferase] S-pent-4-enoyldihydrolipoyllysine + CO2
-
2-oxo-5-hexenoic acid is not a substrate for wild-type
-
-
?
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine
[dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2
-
-
-
-
?
2-oxovalerate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine
[dihydrolipoyllysine-residue succinyltransferase] S-butanoyldihydrolipoyllysine + CO2
-
2-oxovalerate is not a substrate for wild-type
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine
[dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2
-
-
-
?
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine
[dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.11
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-S333M, pH not specified in the publication, temperature not specified in the publication
-
0.5
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-H348F, pH not specified in the publication, temperature not specified in the publication
-
0.73
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-H348Y, pH not specified in the publication, temperature not specified in the publication
-
1.1
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-H348Q, pH not specified in the publication, temperature not specified in the publication
-
0.02
2-oxoglutarate
-
mutant E1o-H298D/E2o-H348Y, pH not specified in the publication, temperature not specified in the publication
0.03
2-oxoglutarate
-
mutant E1o-H298D, pH not specified in the publication, temperature not specified in the publication
0.03
2-oxoglutarate
-
mutant E1o-H298D/E2o-H348F, pH not specified in the publication, temperature not specified in the publication
0.04
2-oxoglutarate
-
wild-type, pH not specified in the publication, temperature not specified in the publication
0.04
2-oxoglutarate
-
mutant E1o-H298D/E2o-S333M, pH not specified in the publication, temperature not specified in the publication
0.07
2-oxoglutarate
-
mutant E1o-H298D/E2o-H348Q, pH not specified in the publication, temperature not specified in the publication
0.01
2-oxovalerate
-
mutant E1o-H298D/E2o-H348F, pH not specified in the publication, temperature not specified in the publication
0.01
2-oxovalerate
-
mutant E1o-H298D/E2o-H348Y, pH not specified in the publication, temperature not specified in the publication
0.05
2-oxovalerate
-
mutant E1o-H298D/E2o-H348Q, pH not specified in the publication, temperature not specified in the publication
0.08
2-oxovalerate
-
mutant E1o-H298D/E2o-S333M, pH not specified in the publication, temperature not specified in the publication
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.65
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-H348Q, pH not specified in the publication, temperature not specified in the publication
-
0.86
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-H348Y, pH not specified in the publication, temperature not specified in the publication
-
0.99
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-H348F, pH not specified in the publication, temperature not specified in the publication
-
1.68
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-S333M, pH not specified in the publication, temperature not specified in the publication
-
6.8
2-oxoglutarate
-
mutant E1o-H298D/E2o-H348Y, pH not specified in the publication, temperature not specified in the publication
7.3
2-oxoglutarate
-
mutant E1o-H298D/E2o-H348F, pH not specified in the publication, temperature not specified in the publication
8.4
2-oxoglutarate
-
mutant E1o-H298D/E2o-S333M, pH not specified in the publication, temperature not specified in the publication
10.5
2-oxoglutarate
-
mutant E1o-H298D/E2o-H348Q, pH not specified in the publication, temperature not specified in the publication
21.1
2-oxoglutarate
-
mutant E1o-H298D, pH not specified in the publication, temperature not specified in the publication
35
2-oxoglutarate
-
wild-type, pH not specified in the publication, temperature not specified in the publication
0.34
2-oxovalerate
-
mutant E1o-H298D/E2o-H348Q, pH not specified in the publication, temperature not specified in the publication
0.38
2-oxovalerate
-
mutant E1o-H298D/E2o-S333M, pH not specified in the publication, temperature not specified in the publication
0.57
2-oxovalerate
-
mutant E1o-H298D/E2o-H348Y, pH not specified in the publication, temperature not specified in the publication
0.81
2-oxovalerate
-
mutant E1o-H298D/E2o-H348F, pH not specified in the publication, temperature not specified in the publication
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.59
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-H348Q, pH not specified in the publication, temperature not specified in the publication
-
1.17
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-H348Y, pH not specified in the publication, temperature not specified in the publication
-
1.98
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-H348F, pH not specified in the publication, temperature not specified in the publication
-
15.3
2-oxo-5-hexenoic acid
-
mutant E1o-H298D/E2o-S333M, pH not specified in the publication, temperature not specified in the publication
-
149
2-oxoglutarate
-
mutant E1o-H298D/E2o-H348Q, pH not specified in the publication, temperature not specified in the publication
210
2-oxoglutarate
-
mutant E1o-H298D/E2o-S333M, pH not specified in the publication, temperature not specified in the publication
244
2-oxoglutarate
-
mutant E1o-H298D/E2o-H348F, pH not specified in the publication, temperature not specified in the publication
338
2-oxoglutarate
-
mutant E1o-H298D/E2o-H348Y, pH not specified in the publication, temperature not specified in the publication
703
2-oxoglutarate
-
mutant E1o-H298D, pH not specified in the publication, temperature not specified in the publication
875
2-oxoglutarate
-
wild-type, pH not specified in the publication, temperature not specified in the publication
4.7
2-oxovalerate
-
mutant E1o-H298D/E2o-S333M, pH not specified in the publication, temperature not specified in the publication
6.8
2-oxovalerate
-
mutant E1o-H298D/E2o-H348Q, pH not specified in the publication, temperature not specified in the publication
57
2-oxovalerate
-
mutant E1o-H298D/E2o-H348Y, pH not specified in the publication, temperature not specified in the publication
81
2-oxovalerate
-
mutant E1o-H298D/E2o-H348F, pH not specified in the publication, temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.0168
-
wild type enzyme, with 2-oxo-5-hexenoate as substrate, at pH 8.0 and 30°C
0.042
-
mutant enzyme H298D, with 2-oxo-5-hexenoate as substrate, at pH 8.0 and 30°C
0.0429
-
wild type enzyme, with 2-oxovalerate as substrate, at pH 8.0 and 30°C
0.135
-
mutant enzyme H298D, with 2-oxovalerate as substrate, at pH 8.0 and 30°C
0.206
-
mutant enzyme H298D, with 2-oxoglutarate as substrate, at pH 8.0 and 30°C
0.775
-
wild type enzyme, with 2-oxoglutarate as substrate, at pH 8.0 and 30°C
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
i.e. SucA, subunit E1 of the 2-oxoglutarate dehydrogenase complex
Uniprot
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
104805
-
x * 104805, 2-oxoglutarate dehydrogenase subunit, calculation from nucleotide sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
-
x * 104805, 2-oxoglutarate dehydrogenase subunit, calculation from nucleotide sequence
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
sitting drop vapour diffusion method with 12% (w/v) polyethylene glycol 4000, 50 mM sodium citrate (pH 5.6)
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H298D
H348F
-
mutation in subunit Eo, leads to activity for 2-oxovalerate in the reconstituted complex with E1o-H298D
H348Q
-
mutation in subunit Eo, leads to activity for 2-oxovalerate in the reconstituted complex with E1o-H298D
H348Y
-
mutation in subunit Eo, leads to activity for 2-oxovalerate in the reconstituted complex with E1o-H298D
S333M
-
mutation in subunit Eo, leads to activity for 2-oxovalerate in the reconstituted complex with E1o-H298D
additional information
-
conversion of enzyme from a 2-oxoglutarate dehydrogenase to a 2-oxo aliphatic dehydrogenase complex by evolving the E1o and E2o components. Mutants E2o-S333M, E2o-H348F, E2o-H348Q, and E2o-H348Y show activity for 2-oxovalerate in the reconstituted complex with E1o-H298D
H298D
-
mutation in subunit E1o, active for 2-oxovalerate in an E1o-specific assay
H298D
-
the mutant enzyme shows 4.4fold increased activity toward 2-oxovalerate and 1200fold decreased activity toward 2-oxoglutarate compared to the wild type enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation, HiLoad Q-Sepharose column chromatography, and Superdex S200 gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
expression of the structural genes for all three subunits of the Escherichia coli 2-oxoglutarate dehydrogenase complex in Saccharomyces cerevisiae. The Escherichia coli lipoic-acid scavenging enzyme is coexpressed to enable cytosolic lipoylation of the complex, which is required for its enzymatic activity. In vivo cytosolic activity of the complex is tested by constructing a reporter strain in which the essential metabolite 5-aminolevulinic acid can only be synthetized from cytosolic, and not mitochondrial, succinyl-CoA. In the resulting strain, complementation of 5-aminolevulinic acid auxotrophy depends on activation of the 2-oxoglutarate dehydrogenase complex by lipoic acid addition
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Guest, J.R.; Darlison, M.G.; Spencer, M.E.; Stephens, P.E.
Cloning and sequence analysis of the pyruvate and 2-oxoglutarate dehydrogenase complex genes of Escherichia coli
Biochem. Soc. Trans.
12
220-223
1984
Escherichia coli
Jones, D.D.; Perham, R.N.
The role of loop and beta-turn residues as structural and functional determinants for the lipoyl domain from the Escherichia coli 2-oxoglutarate dehydrogenase complex
Biochem. J.
409
357-366
2008
Escherichia coli
Frank, R.A.; Price, A.J.; Northrop, F.D.; Perham, R.N.; Luisi, B.F.
Crystal structure of the E1 component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex
J. Mol. Biol.
368
639-651
2007
Escherichia coli (P0AFG3), Escherichia coli
Chakraborty, J.; Nemeria, N.; Zhang, X.; Nareddy, P.; Szostak, M.; Farinas, E.; Jordan, F.
Engineering 2-oxoglutarate dehydrogenase to a 2-oxo aliphatic dehydrogenase complex by optimizing consecutive components
AIChE J.
66
e16769
2020
Escherichia coli
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EXTERNAL LINKS (specific for EC-Number 1.2.4.2)
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