Information on EC 1.3.99.1 - succinate dehydrogenase

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

EC NUMBER
COMMENTARY
1.3.99.1
deleted, the activty is included in EC 1.3.5.1, succinate dehydrogenase (quinone)
RECOMMENDED NAME
GeneOntology No.
succinate dehydrogenase
PATHWAY
KEGG Link
MetaCyc Link
Biosynthesis of secondary metabolites
-
Butanoate metabolism
-
Carbon fixation pathways in prokaryotes
-
Citrate cycle (TCA cycle)
-
Metabolic pathways
-
Microbial metabolism in diverse environments
-
Oxidative phosphorylation
-
Toluene degradation
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
iron-sulfur subunit of succinate dehydrogenase
D2KQI9
-
SDG
Sphaerotilus natans D-507
-
-
-
SDG-1
Sphaerotilus natans D-507
-
-
-
SDG-2
Sphaerotilus natans D-507
-
-
-
SDH2
Saccharomyces cerevisiae BY4742
-
-
-
SdhA
Q9C4L9
succinate dehydrogenase subunit A
SDHB
Helicobasidium mompa V18
E2RZU1
-
-
succinate dehydrogenase iron-sulphur protein
E2RZU1
UniProt
succinate dehydrogenase iron-sulphur protein
Helicobasidium mompa V18
E2RZU1
UniProt
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
single copy sdhB gene, encoding the iron-sulfur protein (Ip) subunit of succinate dehydrogenase, Sdh
UniProt
Manually annotated by BRENDA team
Helicobasidium mompa V18
single copy sdhB gene, encoding the iron-sulfur protein (Ip) subunit of succinate dehydrogenase, Sdh
UniProt
Manually annotated by BRENDA team
Saccharomyces cerevisiae BY4742
gene sdh2s
-
-
Manually annotated by BRENDA team
gene SDH2-2, encoding the iron sulfur subunit of the succinate dehydrogenase protein complex
UniProt
Manually annotated by BRENDA team
two SDG isoforms with different electrophoretic mobility
-
-
Manually annotated by BRENDA team
Sphaerotilus natans D-507
two SDG isoforms with different electrophoretic mobility
-
-
Manually annotated by BRENDA team
gene sdh1-2
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
malfunction
-
succinate production for the SDH-negative Saccharomyces cerevisiae is very low even under fully aerobic conditions, additional zinc finger proteins Mig1 and Mig2 deletion does not result in an increase in succinate production in the SDH-negative strain
malfunction
-
mutation of Arg582 in Sdh1 precludes flavinylation as well as assembly of the tetrameric enzyme complex. Mutation of Arg638 compromises SDH function only when present in combination with a Cys630 substitution. Mutations of either Arg582 or Arg638/Cys630 do not markedly destabilize the Sdh1 polypeptide. The steady-state level of Sdh5 is markedly attenuated in the Sdh1 mutant cells. Truncation of its last 13 residues of Sdh1 abrogates this heme binding and renders the cells respiratory defective
malfunction
D2KQI9
when the Sl SDH2-2 gene is repressed by antisense RNA in a guard cell–specific manner, changes in neither stomatal aperture nor photosynthesis are observed. Antisense SDH transgenic tomato plants exhibit elevated aerial growth and fruit yield, growth phenotype, overview. Inhibition of succinate dehydrogenase results in a reduced flux through the TCA cycle
malfunction
Saccharomyces cerevisiae BY4742
-
succinate production for the SDH-negative Saccharomyces cerevisiae is very low even under fully aerobic conditions, additional zinc finger proteins Mig1 and Mig2 deletion does not result in an increase in succinate production in the SDH-negative strain
-
metabolism
-
phytochrome A participates in the regulation of mitochondrial respiration through effect on SDH expression. White or red light are down-regulating factors for the mRNA content of the sdh1-2 and sdh2-3 genes and SDH catalytic activity both in wild-type plants and in the mutant deficient in the phytochrome B gene, but not in the mutant deficient in the phytochrome A gene, while the far red light of 730 nm reverses the red light effect
metabolism
-
SDH inhibition plays a role in metabolic suppression during hibernation and topor, overview. Oxaloacetate reversibly inhibits SDH in torpor, but cannot fully account for the drastic metabolic suppression observed during this hibernation phase. During arousal from the torpor phase of hibernation this suppression is reversed and metabolic rates rise dramatically
metabolism
-
the enzyme plays a key role in the regulation of aerobic respiration
physiological function
-
SDH is located in the inner membrane of mitochondria and its activity is connected with the operation of the electron transport chain, where it functions as a succinate:ubiquinone reductase, EC 1.3.5.1
physiological function
-
succinate dehydrogenase is part of the nonoxidative branch of the TCA cycle and is directly linked to the respiratory chain. This enzyme complex catalyzes the oxidation of succinate to fumarate, donating FADH2 for oxidative phosphorylation
physiological function
-
SDH catalyzes the oxidation of succinate to fumarate in the matrix of the mitochondrion, donating electrons to ubiquinone that subsequently enter into the electron transport chain
physiological function
-
role of calcium cations in the mechanism of phytochrome-dependent regulation of the sdh1-2 gene expression and succinate dehydrogenase activity in maize leaves, overview. Higher content of calcium cations in the nucleus correlates with the lower level of the sdh1-2 gene transcription, regulation, overview
physiological function
Staphylococcus aureus HG001, Staphylococcus aureus SA113
-
succinate dehydrogenase is part of the nonoxidative branch of the TCA cycle and is directly linked to the respiratory chain. This enzyme complex catalyzes the oxidation of succinate to fumarate, donating FADH2 for oxidative phosphorylation
-
metabolism
Sphaerotilus natans D-507
-
the enzyme plays a key role in the regulation of aerobic respiration
-
additional information
-
regulation of succinate dehydrogenase activity by SIRT3, a member of the sirtuin family of NAD+-dependent deacetylases, in mammalian mitochondria, the hydrophilic surface of SdhA may control the entry of the substrate into the active site of the protein and regulate the enzyme activity. The succinate dehydrogenase flavoprotein, SdhA, subunit is a substrate of SIRT3. Stimulation of SIRT3 expression decreases the level of acetylation of the SdhA subunit and increases Complex II activity in kaempherol-treated cells compared to control and nicotinamide-treated cells
additional information
-
compared to the wild type, the mutant sdhCAB deletion mutant DELTAsdh is impaired in planktonic growth under aerobic conditions, excreted acetic acid can not be reused and accumulated continuously. Succinate is excreted and found in the culture supernatant, and metabolome analysis with cells grown in chemically defined medium reveals reduced uptake/metabolism of some amino acids from the growth medium. Moreover, the mutant is able to counteract the steadily decreasing extracellular pH by increased urease activity. The addition of fumarate to the growth medium restored the wild-type phenotype. The mutant shows a small-colony variant-like phenotype, a slight increase in resistance to various aminoglycoside antibiotics, decreased pigmentation, and decreased growth under aerobic conditions due to the interruption of the TCA cycle, phenotype, overview
additional information
-
the catalytic core Sdh1 and Sdh2 subunits contain the redox cofactors that participate in electron transfer to ubiquinone. Sdh1 contains the covalently bound FAD cofactor and the binding site for succinate. Sdh2 contains the three Fe-S centers that mediate electron transfer to ubiquinone in the complex of succinate-ubiquinone dehydrogenase, EC 1.3.5.1, regulation of SDH, overview. The Leigh syndrome, also known as subacute necrotizing encephalomyelopathy, is an early-onset progressive neurodegenerative disorder, associated with impaired SDH activity due to mutations, e.g. G555E, mechanism of the disease, overview. Mutations in SDHB,-C, and -D are asscoiated with tumor formation, overview
additional information
-
succinate dehydrogenase forms the peripheral part of the Succinate-ubiquinone oxidoreductase, EC 1.3.5.1, and is composed of a flavoprotein, SdhA, and an iron-sulfur protein, SdhB; succinate dehydrogenase forms the peripheral part of the Succinate-ubiquinone oxidoreductase, EC 1.3.5.1, and is composed of a flavoprotein, SdhA, and an iron-sulfur protein, SdhB
additional information
E2RZU1
the I subunit contains three well-conserved cysteine-rich clusters associated with the iron-sulfur centers involved in electron transport
additional information
-
flavinylation and assembly of succinate dehydrogenase are dependent on the C-terminal tail of the flavoprotein subunit, overview. SDH assembly appears to require FAD binding but not necessarily covalent FAD attachment. FAD binding is important to stabilize the Sdh1 conformation enabling association with Sdh2 and the membrane anchor subunits
additional information
-
protein SDHA F2 factor is needed for assembly and activity of SDH and also for normal root elongation, sequence diversity and conservation of SDHA F2 across kingdoms, phylogenetic analysis, overview
additional information
Helicobasidium mompa V18
-
the I subunit contains three well-conserved cysteine-rich clusters associated with the iron-sulfur centers involved in electron transport
-
additional information
Staphylococcus aureus HG001, Staphylococcus aureus SA113
-
compared to the wild type, the mutant sdhCAB deletion mutant DELTAsdh is impaired in planktonic growth under aerobic conditions, excreted acetic acid can not be reused and accumulated continuously. Succinate is excreted and found in the culture supernatant, and metabolome analysis with cells grown in chemically defined medium reveals reduced uptake/metabolism of some amino acids from the growth medium. Moreover, the mutant is able to counteract the steadily decreasing extracellular pH by increased urease activity. The addition of fumarate to the growth medium restored the wild-type phenotype. The mutant shows a small-colony variant-like phenotype, a slight increase in resistance to various aminoglycoside antibiotics, decreased pigmentation, and decreased growth under aerobic conditions due to the interruption of the TCA cycle, phenotype, overview
-
additional information
Xanthomonas oryzae pv. oryzae ZJ173
-
succinate dehydrogenase forms the peripheral part of the Succinate-ubiquinone oxidoreductase, EC 1.3.5.1, and is composed of a flavoprotein, SdhA, and an iron-sulfur protein, SdhB; succinate dehydrogenase forms the peripheral part of the Succinate-ubiquinone oxidoreductase, EC 1.3.5.1, and is composed of a flavoprotein, SdhA, and an iron-sulfur protein, SdhB
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
fumarate + reduced acceptor
succinate + acceptor
show the reaction diagram
-
the obligate autotroph requires fumarate reductase activity if it performs CO2 fixation via a reductive citric acid cycle
-
-
r
fumarate + reduced benzyl viologen
succinate + oxidized benzyl viologen
show the reaction diagram
-
-
-
-
r
succinate + oxidized 2,6-dichlorophenolindophenol
fumarate + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
-
-
-
-
r
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
fumarate + reduced acceptor
succinate + acceptor
show the reaction diagram
-
the obligate autotroph requires fumarate reductase activity if it performs CO2 fixation via a reductive citric acid cycle
-
-
r
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
FAD
-
FAD of Sdh1 is covalently attached at an active site His residue, 8alpha-N3-histidyl-FAD linkage, involving Arg582, required for enzyme activity. Flavinylation and assembly of succinate dehydrogenase are dependent on the C-terminal tail of the flavoprotein subunit. FAD binding is important to stabilize the Sdh1 conformation enabling association with Sdh2 and the membrane anchor subunits
FAD
-
flavinylation of SDH is dependent on SDH1:SDHA F2 interaction requiring the C-terminal tail of SDH1
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Br-
-
activates
Ca2+
-
activates
Ca2+
-
role of calcium cations in the mechanism of phytochrome-dependent regulation of the sdh1-2 gene expression and succinate dehydrogenase activity in maize leaves, overview
Cl-
-
activates
Fe2+
E2RZU1
the protein contains three well-conserved cysteine-rich clusters associated with the iron-sulfur centers involved in electron transport. One of these clusters contains a critical histidine residue implicated in carboxin sensitivity in the basidiomycetes
Fe2+
D2KQI9
iron sulfur subunit of the succinate dehydrogenase protein complex
Iron-sulfur cluster
-
the enzyme has an unusual iron-sulfur cluster composition with respect to that of the canonical succinate dehydrogenases. Center S3, the succinate responsive [3Fe-4S]1+/0 cluster of succinate dehydrogenases, is not present in membranes prepared from aerobically grown Acidianus ambivalens, nor in partially purified complex fractions. It is replaced by a second [4Fe-4S] center, by incorporation of an additional cysteine, at the cysteine cluster binding motif (CxxYxxCxxxC-->CxxCxxCxxxC). The remaining centers, clusters S1 ([2Fe-2S]1+/2+) and S2 ([4Fe-4S]2+/1+), can be observed
Iron-sulfur cluster
-
the enzyme has an unusual iron-sulfur cluster composition with respect to that of the canonical succinate dehydrogenases. Center S3, the succinate responsive [3Fe-4S]1+/0 cluster of succinate dehydrogenases, is not present. The remaining centers, clusters S1 ([2Fe-2S]1+/2+) and S2 ([4Fe-4S]2+/1+), can be observed
Iron-sulfur cluster
-
the enzyme has an unusual iron-sulfur cluster composition in respect to that of the canonical succinate dehydrogenases. Center S3, the succinate responsive [3Fe-4S]1+/0 cluster of succinate dehydrogenases, is not present. The remaining centers, clusters S1 ([2Fe-2S]1+/2+) and S2 ([4Fe-4S]2+/1+), can be observed
K+
-
activates
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
2-oxoglutarate
-
-
oxaloacetic acid
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
alpha-glycerophosphate
-
-
beta-oxybutyric acid
-
-
-
protein SDHA F2
-
the factor is needed for assembly and activity of SDH and also for normal root elongation, sequence diversity and conservation of SDHA F2 across kingdoms, phylogenetic analysis, overview
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.06
-
fumarate
-
pH 6.5, 70°C, detergent treated membranes from aerobic growth
0.08
-
fumarate
-
pH 6.5, 70°C, detergent treated membranes from anaerobic growth
0.3
-
succinate
-
pH 6.5, 70°C, detergent treated membranes from anaerobic growth
0.5
-
succinate
-
pH 6.5, 70°C, detergent treated membranes from aerobic growth
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6.5
-
-
assay at
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
70
-
-
assay at
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
Sphaerotilus natans D-507
-
bound
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
tetramer
-
the enzyme complex consits of four subunits: a flavoprotein SDH1, an iron-sulfur protein SDH2, two integral membrane subunits SDH3 and SDH4. Protein SDHA F2 is needed for assembly and activity of SDH and also for normal root elongation
?
Q9C4L9
x * 63000, SDS-PAGE
additional information
-
the enzyme is part of the tetrameric succinate dehydrogenase complex
additional information
Sphaerotilus natans D-507
-
the enzyme is part of the tetrameric succinate dehydrogenase complex
-
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
flavoprotein
Q9C4L9
covalent flavinylation of succinate dehydrogenase subunit A requires heat and dicarboxylic acids
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
native enzyme by ammonium sulfate fractionation and gel filtration followed by anion exchange chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
gene sdhB, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic analysis
E2RZU1
gene sdh2, disruption of the SDH2 gene and transformation into the sdh1 mutant strain, resulting in SDH-negative strain B2S
-
gene SDH2-2, expression analysis, antisense expressionin transgenic Solanum lycopersicumplants by Agrobacterium tumefaciens-mediated transformation
D2KQI9
EXPRESSION
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
white or red light are down-regulating factors for the mRNA content of the sdh1-2 and sdh2-3 genes and SDH catalytic activity both in wild-type plants and in the mutant deficient in the phytochrome B gene, but not in the mutant deficient in the phytochrome A gene, while the far red light of 730 nm reverses the red light effect
-
transcriptional regulation: the cAMP-dependent regulator GlxR functions as a repressor sdhCAB operon expression
-
transcriptional regulation: the regulator of acetate metabolism RamAas functions an activator of sdhCAB operon expression, whereas RamB has no obvious influence
-
treatment of K-562 cell lines with nicotinamide and kaempferol to inhibit deacetylase activity of SIRT3 and stimulate SIRT3 expression, overview
-
Hfq protein binds NrrF (a Fur-regulated sRNA) and mediates Fur-dependent NrrF regulation of succinate dehydrogenase. NrrF forms a duplex with a region of complementarity within the sdhDA region of the succinate dehydrogenase transcript, and Hfq enhances the binding of this sRNA to the identified target in the sdhCDAB mRNA. This is likely to result in rapid turnover of the transcript in vivo
-
higher content of calcium cations in the nucleus correlates with the lower level of the sdh1-2 gene transcription, regulation, overview
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
C630A/R638A
-
naturally occuring mutant, overexpression of Sdh5 partially does not restore growth of the double mutant
R582A
-
site-directed mutagenesis, inactive mutant, no growth without glucose
R582A/M599R
-
the mutant shows slightly reduced growth without glucose
R582C
-
site-directed mutagenesis, the mutant shows slightly reduced growth without glucose
R582W
-
naturally occuring mutant, inactive Sdh1 mutant; site-directed mutagenesis, inactive mutant, no growth without glucose
G70V/R638A
-
naturally occuring Sdh1 mutant, the mutant shows slightly reduced growth without glucose
additional information
-
construction of several SDH subunit deletion strains, overview. Truncation of its last 13 residues of sdh1 abrogates this heme binding and renders the cells respiratory defective. Mutation of Arg638 compromises SDH function only when present in combination with a Cys630 substitution. Mutations of either Arg582 or Arg638/Cys630 do not markedly destabilize the Sdh1 polypeptide. The steady-state level of Sdh5 is markedly attenuated in the Sdh1 mutant cells
R638A
-
naturally occuring mutant, the mutant shows highly reduced growth without glucose, overexpression of Sdh5 partially restores growth of the single R638A mutant
additional information
D2KQI9
expression of a fragment of the Sl SDH2-2 gene encoding the iron sulfur subunit of the succinate dehydrogenase protein complex in the antisense orientation under the control of the 35S promoter leads to an enhanced rate of photosynthesis. When the Sl SDH2-2 gene is repressed by antisense RNA in a guard cell-specific manner, changes in neither stomatal aperture nor photosynthesis are observed. Antisense SDH transgenic tomato plants exhibit elevated aerial growth and fruit yield, growth phenotype, overview