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Information on EC 1.3.8.12 - (2S)-methylsuccinyl-CoA dehydrogenase
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1.3.8.12 (2S)-methylsuccinyl-CoA dehydrogenaseIUBMB Comments
The enzyme, characterized from the bacterium Rhodobacter sphaeroides, is involved in the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. The enzyme contains FAD.
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
Synonyms
(2s)-methylsuccinyl-coa dehydrogenase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
MCD
methylsuccinyl-CoA dehydrogenase
PdMCD
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein = 2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
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PATHWAY SOURCE
PATHWAYS
BRENDA
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-
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SYSTEMATIC NAME
IUBMB Comments
(2S)-methylsuccinyl-CoA:electron-transfer flavoprotein oxidoreductase
The enzyme, characterized from the bacterium Rhodobacter sphaeroides, is involved in the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. The enzyme contains FAD.
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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
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein
2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
(2S)-methylsuccinyl-CoA + ferrocenium hexafluorophosphate
mesaconyl-CoA + ferricenium hexafluorophosphate
succinyl-CoA + electron-transfer flavoprotein
fumaryl-CoA + reduced electron-transfer flavoprotein
succinyl-CoA + ferrocenium hexafluorophosphate
fumaryl-CoA + ferricenium hexafluorophosphate
the enzyme shows about 0.5% activity with succinyl-CoA
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-
?
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein
2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
-
-
-
?
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein
2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
the enzyme is involved ion the ethylmalonyl-CoA pathway for acetyl-CoA assimilation
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-
?
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein
2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
the enzyme is highly specific for (S)-methylsuccinyl-CoA. No activity with butyryl-CoA, isobutyryl-CoA or a diastereomeric mixture of (R)-methylsuccinyl-CoA
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-
?
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein
2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
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-
-
?
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein
2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
-
-
-
?
(2S)-methylsuccinyl-CoA + ferrocenium hexafluorophosphate
mesaconyl-CoA + ferricenium hexafluorophosphate
the enzyme is highly specific for (2S)-methylsuccinyl-CoA
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-
?
(2S)-methylsuccinyl-CoA + ferrocenium hexafluorophosphate
mesaconyl-CoA + ferricenium hexafluorophosphate
the enzyme is highly specific for (2S)-methylsuccinyl-CoA
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-
?
succinyl-CoA + electron-transfer flavoprotein
fumaryl-CoA + reduced electron-transfer flavoprotein
low activity
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-
?
succinyl-CoA + electron-transfer flavoprotein
fumaryl-CoA + reduced electron-transfer flavoprotein
low activity
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-
?
additional information
?
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FAD does not dissociate from the enzyme during catalysis. The reaction product can only be released after FAD is re-oxidized within the active site by a final electron acceptor
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-
-
additional information
?
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substrate specificity of methylsuccinyl-CoA dehydrogenase, structure-function analysis, overview. The enzyme catalyzes the oxidation of (2S)-methylsuccinyl-CoA to alpha,beta-unsaturated mesaconyl-CoA and shows only about 0.5% activity with succinyl-CoA. MCD catalyzes the unprecedented oxidation of an alpha-methyl branched dicarboxylic acid CoA thioester. Substrate specificity is achieved by a cluster of three arginines that accommodates the terminal carboxyl group and a dedicated cavity that facilitates binding of the C2 methyl branch. The alpha,beta-desaturation of the CoA thioester is initiated by a proton abstraction from the alpha-carbon by a conserved catalytically active glutamate and a hydride transfer from the beta-carbon to the N5 of the FAD cofactor. The reduced cofactor is reoxidized by two sequential one-electron transfers to electron transfer flavoproteins (ETFs), which in turn deliver the electrons to the membrane-bound electron transport chain for energy conservation
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-
-
additional information
?
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the enzyme has no detectable activity toward (2R)-methylsuccinyl-CoA, butyryl-CoA, and isobutyryl-CoA
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-
additional information
?
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substrate specificity of methylsuccinyl-CoA dehydrogenase, structure-function analysis, overview. The enzyme catalyzes the oxidation of (2S)-methylsuccinyl-CoA to alpha,beta-unsaturated mesaconyl-CoA and shows only about 0.5% activity with succinyl-CoA. MCD catalyzes the unprecedented oxidation of an alpha-methyl branched dicarboxylic acid CoA thioester. Substrate specificity is achieved by a cluster of three arginines that accommodates the terminal carboxyl group and a dedicated cavity that facilitates binding of the C2 methyl branch. The alpha,beta-desaturation of the CoA thioester is initiated by a proton abstraction from the alpha-carbon by a conserved catalytically active glutamate and a hydride transfer from the beta-carbon to the N5 of the FAD cofactor. The reduced cofactor is reoxidized by two sequential one-electron transfers to electron transfer flavoproteins (ETFs), which in turn deliver the electrons to the membrane-bound electron transport chain for energy conservation
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-
-
additional information
?
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the enzyme has no detectable activity toward (2R)-methylsuccinyl-CoA, butyryl-CoA, and isobutyryl-CoA
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-
-
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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
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein
2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein
2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
-
-
-
?
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein
2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
the enzyme is involved ion the ethylmalonyl-CoA pathway for acetyl-CoA assimilation
-
-
?
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein
2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
-
-
-
?
(2S)-methylsuccinyl-CoA + electron-transfer flavoprotein
2-methylfumaryl-CoA + reduced electron-transfer flavoprotein
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
electron transferring flavoprotein
ETF, recombinant EtfA and EtfB from Rhodobacter sphaeroides by expression in Escherichia coli strain BL21(DE3)
FAD
the enzyme contains 0.7 mol of noncovalently bound FAD molecule per subunit
FAD
FAD cofactor is bound in both active sites of the homodimer
FAD
required prosthetic group, FAD does not dissociate from the enzyme during catalysis. The reaction product can only be released after FAD is re-oxidized within the active site by a final electron acceptor
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
Michaelis-Menten kinetics
-
0.064
(2S)-methylsuccinyl-CoA
recombinant mutant A282V, pH 7.5, 30°C
0.064
(2S)-methylsuccinyl-CoA
mutant enzyme A282V, at pH 7.5 and 30°C
0.08
(2S)-methylsuccinyl-CoA
recombinant wild-type enzyme, pH 7.5, 30°C
0.08
(2S)-methylsuccinyl-CoA
wild type enzyme, at pH 7.5 and 30°C
0.439
(2S)-methylsuccinyl-CoA
recombinant mutant A282F/F284A, pH 7.5, 30°C
0.439
(2S)-methylsuccinyl-CoA
mutant enzyme A282F/F284A, at pH 7.5 and 30°C
0.141
succinyl-CoA
recombinant wild-type enzyme, pH 7.5, 30°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.71
(2S)-methylsuccinyl-CoA
recombinant mutant A282F/F284A, pH 7.5, 30°C
0.71
(2S)-methylsuccinyl-CoA
mutant enzyme A282F/F284A, at pH 7.5 and 30°C
31.8
(2S)-methylsuccinyl-CoA
recombinant mutant A282V, pH 7.5, 30°C
31.8
(2S)-methylsuccinyl-CoA
mutant enzyme A282V, at pH 7.5 and 30°C
82.3
(2S)-methylsuccinyl-CoA
wild type enzyme, at pH 7.5 and 30°C
82.3
(2S)-methylsuccinyl-CoA
recombinant wild-type enzyme, pH 7.5, 30°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.6
(2S)-methylsuccinyl-CoA
mutant enzyme A282F/F284A, at pH 7.5 and 30°C
1.62
(2S)-methylsuccinyl-CoA
recombinant mutant A282F/F284A, pH 7.5, 30°C
496.9
(2S)-methylsuccinyl-CoA
recombinant mutant A282V, pH 7.5, 30°C
500
(2S)-methylsuccinyl-CoA
mutant enzyme A282V, at pH 7.5 and 30°C
1000
(2S)-methylsuccinyl-CoA
wild type enzyme, at pH 7.5 and 30°C
1028.75
(2S)-methylsuccinyl-CoA
recombinant wild-type enzyme, pH 7.5, 30°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
convertion of (2S)-methylsuccinyl-CoA dehydrogenase (Mcd), a member of the ACAD enzyme family, into a (2S)-methylsuccinyl-CoA oxidase (Mco) through three active site mutations
metabolism
physiological function
additional information
evolution
(2S)-methylsuccinyl-CoA dehydrogenase (MCD) belongs to the family of FAD-dependent acyl-CoA dehydrogenase (ACD). Compared with other ACDs, MCD contains an about 170-residue-long N-terminal extension that structurally mimics a dimer-dimer interface of these enzymes that are canonically organized as tetramers. MCD apparently evolved toward preventing the nonspecific oxidation of succinyl-CoA, which is a close structural homologue of (2S)-methylsuccinyl-CoA and an essential intermediate in central carbon metabolism
evolution
the members of the flavin adenosine dinucleotide (FAD)-dependent acyl-CoA dehydrogenase and acyl-CoA oxidase families catalyze similar reactions and share common structural features. But both enzyme families feature opposing reaction specificities in respect to dioxygen. Dehydrogenases react with electron transfer flavoproteins as terminal electron acceptors and do not show a considerable reactivity with dioxygen, whereas dioxygen serves as a bona fide substrate for oxidases
evolution
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(2S)-methylsuccinyl-CoA dehydrogenase (MCD) belongs to the family of FAD-dependent acyl-CoA dehydrogenase (ACD). Compared with other ACDs, MCD contains an about 170-residue-long N-terminal extension that structurally mimics a dimer-dimer interface of these enzymes that are canonically organized as tetramers. MCD apparently evolved toward preventing the nonspecific oxidation of succinyl-CoA, which is a close structural homologue of (2S)-methylsuccinyl-CoA and an essential intermediate in central carbon metabolism
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metabolism
the enzyme is involved in the ethylmalonyl-CoA pathway, an acetyl-CoA assimilation strategy
metabolism
(2S)-methylsuccinyl-CoA dehydrogenase (MCD) is a key enzyme of the ethylmalonyl-CoA pathway for acetate assimilation
metabolism
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(2S)-methylsuccinyl-CoA dehydrogenase (MCD) is a key enzyme of the ethylmalonyl-CoA pathway for acetate assimilation
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physiological function
acyl-CoA dehydrogenases (ACADs) are flavoproteins that catalyze the flavin adenosine dinucleotide (FAD)-dependent oxidation of alpha,beta-carbon bonds in acyl-CoA thioesters. ACADs are found in all kingdoms of life and are part of various metabolic pathways, such as amino acid oxidation, choline metabolism and most prominently, the initial step in fatty acid beta-oxidation. ACADs transfer the electrons from the substrate to an electron transfer flavoprotein (ETF), which in turn funnels the electrons into a membrane bound electron transport chain and from there to the final electron acceptor. The reaction of ACADs can be divided into a reductive and an oxidative half-reaction. The reductive half-reaction is initiated by abstraction of the pro-R-alpha-proton of the acyl-CoA thioester by a conserved active site glutamate. The concomitant hydride transfer of the pro-R-beta-hydrogen to the N5 atom of the isoalloxazine ring of the FAD cofactor proceeds via an enolate-like intermediate, which forms a charge-transfer complex (CTC) with the FAD. Although the substrate is rapidly converted into the CTC, no product is formed in the absence of ETF or another suitable electron acceptor The reaction is completed with the electron transfer from the CTC to ETF during the oxidative half-reaction. The oxidative half-reaction consists of two successive inter-protein one-electron transfers between reduced ACAD and two oxidized ETFs. This results in the re-oxidation of the ACAD bound FAD and yields two ETFs in the semiquinone state (ETFsq). In contrast to ACADs, acyl-CoA oxidases (ACXs) do not require an ETF partner and directly use dioxygen as a final electron acceptor
physiological function
MCD prevents the nonspecific oxidation of succinyl-CoA, which is a close structural homologue of (2S)-methylsuccinyl-CoA and an essential intermediate in central carbon metabolism. Structure-function analysis, overview
physiological function
-
MCD prevents the nonspecific oxidation of succinyl-CoA, which is a close structural homologue of (2S)-methylsuccinyl-CoA and an essential intermediate in central carbon metabolism. Structure-function analysis, overview
-
additional information
active site structure, structure-function analysis, overview
additional information
-
active site structure, structure-function analysis, overview
-
Show AA Sequence and Transmembrane Helices (124 entries)
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Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
62300
2 * 62300, N-terminal histidine-tagged fusion protein, SDS-PAGE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
additional information
homodimer
2 * 62300, N-terminal histidine-tagged fusion protein, SDS-PAGE
additional information
compared with other ACDs, MCD contains an about 170-residue-long N-terminal extension that structurally mimics a dimer-dimer interface of these enzymes that are canonically organized as tetramers
additional information
-
compared with other ACDs, MCD contains an about 170-residue-long N-terminal extension that structurally mimics a dimer-dimer interface of these enzymes that are canonically organized as tetramers
-
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant FAD-bound enzyme, sitting drop vapor diffusion method, mixing of 20 mg/ml protein in 20 mM Tris-HCl, pH 7.9, 200 mM NaCl, 1.5 mM FAD, and 3 mM mesaconyl-CoA in an 1:1 ratio with crystallization solution containing 30% PEG 5000 monomethyl ether mesylate, 100 mM Tris, pH 8.0, and 200 mM LiSO4, 16°C, X-ray diffraction structure determination and analysis at 1.37 A resolution, modeling
sitting drop vapor diffusion method, using 30% (w/v) PEG 5000 monomethyl ether mesylate, 100 mM Tris, pH 8.0, and 200 mM LiSO4
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E377N
site-directed mutagenesis, the mutant does not show increased oxidase activity although reduced dehydrogenase activity compared to wild-type
M375S
site-directed mutagenesis, the mutant is inactive as oxidase
T317G
site-directed mutagenesis, the mutant shows increased oxidase activity and reduced dehydrogenase activity compared to wild-type. The mutant directly reacts with O2
W315F
site-directed mutagenesis, the mutant does not show increased oxidase activity although reduced dehydrogenase activity compared to wild-type
W315F/T317G/E377N
site-directed mutagenesis, the mutant shows increased oxidase activity and reduced dehydrogenase activity compared to wild-type. The mutant directly reacts with O2
Y372I
site-directed mutagenesis, the mutant is inactive as oxidase
Y378G
site-directed mutagenesis, the mutant is inactive as oxidase
A282F
A282F/F284A
A282F/F284L
A282F/F284V
A282I
A282L
A282V
A282L
A282V
additional information
A282F/F284A
site-directed mutagenesis, mutant is inactive with succinyl-CoA, but shows residual activity with (S2)-methylsuccinyl-CoA
A282F/F284A
the double mutant is still able to convert (2S)-methyl-succinyl-CoA, however with less than 0.2% of the relative catalytic efficiency
A282F/F284L
the double mutant does not show any activity with succinyl-CoA
A282F/F284V
the double mutant does not show any activity with succinyl-CoA
A282V
site-directed mutagenesis, the mutant shows increased activity with succinyl-CoA compare to wild-type
A282V
the catalytic efficiency of the variant with (2S)-methylsuccinyl-CoA is decreased by 50% compared with the wild type which is mostly due to a decreased turnover number. On the other hand, the variant exhibits an increased catalytic efficiency with unbranched succinyl-CoA due to a decrease in Km
A282V
-
site-directed mutagenesis, the mutant shows increased activity with succinyl-CoA compare to wild-type
-
A282V
-
the catalytic efficiency of the variant with (2S)-methylsuccinyl-CoA is decreased by 50% compared with the wild type which is mostly due to a decreased turnover number. On the other hand, the variant exhibits an increased catalytic efficiency with unbranched succinyl-CoA due to a decrease in Km
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additional information
(2S)-methylsuccinyl-CoA dehydrogenase is engineered towards oxidase activity by rational mutagenesis. The molecular base for dioxygen reactivity in the engineered oxidase shows that the increased oxidase function of the engineered enzyme comes at a decreased dehydrogenase activity, analysis by using stopped-flow UV-spectroscopy and liquid chromatography-mass spectrometry (LC-MS) based assays. Simply increasing accessibility for dioxygen is not a straight-forward approach to increase the oxidase reactivity in ACADs. Of three single mutants W315F, T317G and E377N only the Mcd variant T317G shows significant oxidase activity. Combination of all three mutations results in a variant with considerable oxidase activity. The three residues (Y372, M375, and Y378) as targets are located in the vicinity of the FAD cofactor. M375 and Y372 cover the isoalloxazine moiety of the FAD to shield it from solvent exposure. An increased solvation of the active site is proposed to increase reactivity towards dioxygen in ACADs due to stabilization of the formed superoxide. Mutation of Y372 and M375 to isoleucine and serine, respectively, is performed because these smaller residues are partially conserved in other ACADs, according to a multiple sequence alignment
additional information
the substrate specificity of MCD is shifted toward succinyl-CoA through active-site mutagenesis
additional information
-
the substrate specificity of MCD is shifted toward succinyl-CoA through active-site mutagenesis
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
HisTrap column chromatography and Superdex 200 gel filtration
recombinant His-tagged wild-tpye and mutant enzymes from Escherichia coli strain Rosetta pLys (DE3) by nickel affinity chromatography of cell-free supernatant, desalting gel filtration, tag cleavage by thrombin, gel filtration, and ultrafiltration
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain Rosetta (DE3) pLysS by nickel affinity chromatography and ultrafiltration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli as a N-terminal histidine-tagged fusion protein
recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain Rosetta (DE3) pLysS
sequence comparisons, recombinant expression of His-tagged wild-tpye and mutant enzymes in Escherichia coli strain Rosetta pLys (DE3)
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Erb, T.J.; Fuchs, G.; Alber, B.E.
(2S)-Methylsuccinyl-CoA dehydrogenase closes the ethylmalonyl-CoA pathway for acetyl-CoA assimilation
Mol. Microbiol.
73
992-1008
2009
Cereibacter sphaeroides (D3JV03), Cereibacter sphaeroides
brenda
Schwander, T.; McLean, R.; Zarzycki, J.; Erb, T.
Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase, an unusual member of the acyl-CoA dehydrogenase family
J. Biol. Chem.
293
1702-1712
2018
Paracoccus denitrificans (A1B5Y0), Paracoccus denitrificans Pd1222 (A1B5Y0)
brenda
Burgener, S.; Schwander, T.; Romero, E.; Fraaije, M.W.; Erb, T.J.
Molecular basis for converting (2S)-methylsuccinyl-CoA dehydrogenase into an oxidase
Molecules
23
68
2017
Cereibacter sphaeroides (D3JV03)
brenda
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Release 2023.1 (January 2023)
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