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 ACCESSION NO.
LITERATURE
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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4-carboxybut-2-enoyl-CoA = but-2-enoyl-CoA + CO2
show the reaction diagram
stereochemistry
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4-carboxybut-2-enoyl-CoA = but-2-enoyl-CoA + CO2
show the reaction diagram
mechanism, interaction of subunits
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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 of carboxy-transfer
Q06700
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
decarboxylation
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-
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PATHWAY
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 degradation V (via hydroxyglutarate)
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glutaryl-CoA degradation
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Microbial metabolism in diverse environments
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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 ACCESSION NO.
COMMENTARY
LITERATURE
carboxyltransferase
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-
-
-
decarboxylase, glutaconyl coenzyme A
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-
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GCD
Clostridium symbiosum HB25
B7TVP1
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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
SEQUENCE CODE
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
-
-
Manually annotated by BRENDA team
enzyme also decarboxylates glutaryl-CoA
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
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 ACCESSION NO.
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
-
-
-
-
?
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 ACCESSION NO.
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 ACCESSION NO.
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
FAD
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1.1 mol of FAD per subunit, Km: 0.00025 mM
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Na+
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Km: 1 mM; required
Na+
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required
Na+
-
Km: 3 mM; required
Na+
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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 ACCESSION NO.
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
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with increasing chain length, sodium ions prevent inactivation, Li+ is ten times less effective than Na+
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ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
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
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]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
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]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0074
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glutaryl-CoA
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-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
48
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cell free extract, pH 7.2, 22C
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
170000
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gel filtration
232000
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B7TVP1
gel filtration
additional information
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in sucrose density gradient centrifugation the activity is recovered in 2 peaks: MW 470000, possibly dimer and MW 250000, possibly monomer
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
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 * 33000, beta, carboxylyase + x * 19000, gamma, biotin carrier + x * 16000, probably carboxylyase, 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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1 * 120000-140000, alpha, contains biotin + 1 * 60000, beta, + 1 * 35000, gamma, hydrophobic, 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
heterotetramer
B7TVP1
1 * 65000 + 1 * 35000 + 1 * 14000 + 1 * 12000, X-ray crystallography
heterotetramer
Clostridium symbiosum HB25
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1 * 65000 + 1 * 35000 + 1 * 14000 + 1 * 12000, X-ray crystallography
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tetramer
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4 * 41000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
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
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
37
-
-
200 mM KCl: 50% loss of activity after 4 min, 200 mM NaCl: 10% loss of activity after 15 min
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
sodium ions specifically protect the gamma chain from tryptic digestion
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requires Na+ for stability
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unstable in the presence of buffers containing potassium
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sodium ions specifically protect the gamma chain from tryptic digestion
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ORGANIC SOLVENT
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
1-butanol
-
concentration 2%, 50% loss of activity after 2 min
1-butanol
-
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 ACCESSION NO.
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 ACCESSION NO.
LITERATURE
Strep-Tactin Sepharose column chromatography, Ni-NTA affinity chromatography, and avidin-biotin affinity chromatography
B7TVP1
subsp. nucleatum
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
four different subunits
-
expressed in Escherichia coli Rosetta (DE3) cells
B7TVP1