Information on EC 4.1.1.70 - glutaconyl-CoA decarboxylase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY
4.1.1.70
-
RECOMMENDED NAME
GeneOntology No.
glutaconyl-CoA decarboxylase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
4-carboxybut-2-enoyl-CoA = but-2-enoyl-CoA + CO2
show the reaction diagram
stereochemistry
-
4-carboxybut-2-enoyl-CoA = but-2-enoyl-CoA + CO2
show the reaction diagram
mechanism of carboxy-transfer
Q06700
4-carboxybut-2-enoyl-CoA = but-2-enoyl-CoA + CO2
show the reaction diagram
energetics
-
4-carboxybut-2-enoyl-CoA = but-2-enoyl-CoA + CO2
show the reaction diagram
mechanism, interaction of subunits
-
4-carboxybut-2-enoyl-CoA = but-2-enoyl-CoA + CO2
show the reaction diagram
the enzyme from Acidaminococcus fermentans is a biotinyl-protein, requires Na+, and acts as a sodium pump. Prior to the Na+-dependent decarboxylation, the carboxlate is transferred to biotin in a Na+-independent manner. The conserved lysine, to which biotin forms an amine bond, is located 34 amino acids before the C-terminus, flanked on both sides by two methionine residues, which are conserved in every biotin-dependent enzyme
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
decarboxylation
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Benzoate degradation
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Butanoate metabolism
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crotonate fermentation (to acetate and cyclohexane carboxylate)
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glutamate and glutamine metabolism
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glutaryl-CoA degradation
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L-glutamate degradation V (via hydroxyglutarate)
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Microbial metabolism in diverse environments
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tryptophan metabolism
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SYSTEMATIC NAME
IUBMB Comments
4-carboxybut-2-enoyl-CoA carboxy-lyase (but-2-enoyl-CoA-forming)
The enzyme from Acidaminococcus fermentans is a biotinyl-protein, requires Na+, and acts as a sodium pump. Prior to the Na+-dependent decarboxylation, the carboxylate is transferred to biotin in a Na+-independent manner. The conserved lysine, to which biotin forms an amide bond, is located 34 amino acids before the C-terminus, flanked on both sides by two methionine residues, which are conserved in every biotin-dependent enzyme.
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
carboxyltransferase
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-
-
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decarboxylase, glutaconyl coenzyme A
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-
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pent-2-enoyl-CoA carboxy-lyase
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-
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CAS REGISTRY NUMBER
COMMENTARY
84399-93-9
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
subunit A; strain HB25
UniProt
Manually annotated by BRENDA team
Clostridium symbiosum HB25
subunit A; strain HB25
UniProt
Manually annotated by BRENDA team
subsp. nucleatum
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-
Manually annotated by BRENDA team
enzyme also decarboxylates glutaryl-CoA
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
B7TVP1
Gcd couples the biotin-dependent decarboxylation of glutaconyl-CoA with the generation of an electrochemical Na+ gradient
physiological function
Clostridium symbiosum HB25
-
Gcd couples the biotin-dependent decarboxylation of glutaconyl-CoA with the generation of an electrochemical Na+ gradient
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SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
4-carboxybut-2-enoyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
4-carboxybut-2-enoyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
4-carboxybut-2-enoyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
4-carboxybut-2-enoyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
4-carboxybut-2-enoyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
4-carboxybut-2-enoyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
4-carboxybut-2-enoyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
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i.e. glutaconyl-CoA
i.e. crotonyl-CoA
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
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-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
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-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
i.e. glutaconyl-CoA
i.e. crotonyl-CoA
?
glutaryl-CoA
butyryl-CoA + CO2
show the reaction diagram
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-
-
-
?
additional information
?
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enzyme catalyzes a 3H exchange of [2,4,4-3H]glutaconate with water when acetyl-CoA is present
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additional information
?
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not: 3-methylglutaconyl-CoA
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additional information
?
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pathway of fermentative benzoate degradation
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
-
-
-
?
glutaconyl-CoA
but-2-enoyl-CoA + CO2
show the reaction diagram
-
i.e. glutaconyl-CoA
i.e. crotonyl-CoA
?
additional information
?
-
-
pathway of fermentative benzoate degradation
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
biotin
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biotinyl enzyme
biotin
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biotinyl enzyme; Km: 40 mM
biotin
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biotinyl enzyme
biotin
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biotinyl enzyme
biotin
B7TVP1
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FAD
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1.1 mol of FAD per subunit, Km: 0.00025 mM
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Na+
-
Km: 1 mM; required
Na+
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required
Na+
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Km: 3 mM; required
Na+
-
activation by Na+ is inhibited by Li+; Km: 1 mM; stimulates
Na+
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activation by Na+ is inhibited by Li+; stimulates
Na+
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Km: 2.5 mM; required
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
N-Alkanols
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concentration required for complete inactivation decreases N-dodecyl-N-dimethylaminoxide at 20-30C
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glutaryl-CoA
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competitive to glutaconyl-CoA
additional information
-
with increasing chain length, sodium ions prevent inactivation, Li+ is ten times less effective than Na+
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
biotin
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biotinyl enzyme
biotin
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biotinyl enzyme; Km: 40 mM
biotin
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biotinyl enzyme
biotin
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biotinyl enzyme
Brij 35
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only Triton X-100 and Brij 35 are able to keep the enzyme in an active state at 20-30C
Phospholipid
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stimulates enzyme
Triton X-100
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only Triton X-100 and Brij 35 are able to keep the enzyme in an active state at 20-30C
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
6 - 11
glutaconyl-CoA
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28C, pH 7.5
3 - 5
glutaryl-CoA
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28C, pH 7.5
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0074
glutaryl-CoA
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
48
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cell free extract, pH 7.2, 22C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
170000
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gel filtration
391416
232000
B7TVP1
gel filtration
704548
additional information
-
in sucrose density gradient centrifugation the activity is recovered in 2 peaks: MW 470000, possibly dimer and MW 250000, possibly monomer
648358
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
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1 * 120000-140000, alpha, contains biotin + 1 * 60000, beta, + 1 * 35000, gamma, hydrophobic, SDS-PAGE
?
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x * 120000, alpha, biotin carrier + x * 60000, beta, carboxytransferase, carboxylase + x * 30000, gamma, sodium pump, SDS-PAGE
?
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x * 120000, alpha, biotin carrier + x * 60000, beta, transferase + x * 30000, gamma, sodium-dependent carboxybiotin decarboxylase, SDS-PAGE
?
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x * 65000, alpha, carboxytransferase, + x * 39000, beta, decarboxylase, + x * 14000, gamma, biotin carrier, + x * 12000, delta, membrane anchor, deduced from gene sequence, expression and purification of alpha leads to a homotrimer, SDS-PAGE
?
-
x * 65000 alpha, carboxytransferase + x * 33000, beta, carboxylyase + x * 19000, gamma, biotin carrier + x * 16000, probably carboxylyase, SDS-PAGE
heterotetramer
B7TVP1
1 * 65000 + 1 * 35000 + 1 * 14000 + 1 * 12000, X-ray crystallography
heterotetramer
Clostridium symbiosum HB25
-
1 * 65000 + 1 * 35000 + 1 * 14000 + 1 * 12000, X-ray crystallography
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tetramer
-
4 * 41000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
subunit alpha, decarboxylase, in complex with glutaconyl-CoA, dimer
Q06700
co-crystallization of the decarboxylase subunit GcdA with the substrate glutaconyl-CoA, the product crotonyl-CoA, and the substrate analogue glutaryl-CoA, sitting drop vapor diffusion method, using in 0.1 M sodium citrate, pH 5.6-6.5, 1 M ammonium phosphate, 27.5% (v/v) glycerol
B7TVP1
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
-
200 mM KCl: 50% loss of activity after 4 min, 200 mM NaCl: 10% loss of activity after 15 min
648355
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
sodium ions specifically protect the gamma chain from tryptic digestion
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requires Na+ for stability
-
unstable in the presence of buffers containing potassium
-
sodium ions specifically protect the gamma chain from tryptic digestion
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ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
1-butanol
-
concentration 2%, 50% loss of activity after 2 min
1-butanol
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concentration 1%, 50% loss of activity after 1 min in presence of 200 mM KCl, 50% loss of activity after 3 min in presence of 200 mM NaCl
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, little loss of activity after 1 year
-
-80C, 24 h, 100 mM Na+, stable
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4C, 24 h, 100 mM Na+, 50% loss of activity
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Strep-Tactin Sepharose column chromatography, Ni-NTA affinity chromatography, and avidin-biotin affinity chromatography
B7TVP1
subsp. nucleatum
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
four different subunits
-
expressed in Escherichia coli Rosetta (DE3) cells
B7TVP1