Information on EC 6.2.1.25 - Benzoate-CoA ligase

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

EC NUMBER
COMMENTARY hide
6.2.1.25
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RECOMMENDED NAME
GeneOntology No.
Benzoate-CoA ligase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + benzoate + CoA = AMP + diphosphate + benzoyl-CoA
show the reaction diagram
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Acid-thiol ligation
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Aminobenzoate degradation
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anaerobic aromatic compound degradation (Thauera aromatica)
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benzoate biosynthesis I (CoA-dependent, beta-oxidative)
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Benzoate degradation
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benzoate degradation II (aerobic and anaerobic)
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Metabolic pathways
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Microbial metabolism in diverse environments
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non-pathway related
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salicortin biosynthesis
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tetrahydroxyxanthone biosynthesis (from benzoate)
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SYSTEMATIC NAME
IUBMB Comments
Benzoate:CoA ligase (AMP-forming)
Also acts on 2-, 3- and 4-fluorobenzoate, but only very slowly on the corresponding chlorobenzoates.
CAS REGISTRY NUMBER
COMMENTARY hide
95329-17-2
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Anaerobic bacterium
a strictly anaerobic, obligate synthrophic mixed culture
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Manually annotated by BRENDA team
CIB
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Manually annotated by BRENDA team
CIB
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Manually annotated by BRENDA team
gram-negative, nitrate-reducing strain Asl-3
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Manually annotated by BRENDA team
Burkholderia xenovorans
strain LB400
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Manually annotated by BRENDA team
annual California plant
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Manually annotated by BRENDA team
Geobacter metallireducens strain GS-15
ATCC 53774, DSM 7210
UniProt
Manually annotated by BRENDA team
strainTS-6
TrEMBL
Manually annotated by BRENDA team
strainTS-6
TrEMBL
Manually annotated by BRENDA team
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Manually annotated by BRENDA team
strain KB740
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Manually annotated by BRENDA team
male Wistar LAT1
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Manually annotated by BRENDA team
strain SB, in syntropic association with Methanospillum hungatei strain JF1
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Manually annotated by BRENDA team
diverse mutant strains, gene xabE
UniProt
Manually annotated by BRENDA team
diverse mutant strains, gene xabE
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + 2-aminobenzoate + CoA
AMP + diphosphate + 2-aminobenzoyl-CoA
show the reaction diagram
ATP + 2-chlorobenzoate + CoA
AMP + diphosphate + 2-chlorobenzoyl-CoA
show the reaction diagram
ATP + 2-fluorobenzoate + CoA
AMP + diphosphate + 2-fluorobenzoyl-CoA
show the reaction diagram
ATP + 2-hydroxybenzoate + CoA
AMP + diphosphate + 2-hydroxybenzoyl-CoA
show the reaction diagram
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15% of the activity relative to benzoate
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?
ATP + 2-methylbenzoate + CoA
AMP + diphosphate + 2-methylbenzoyl-CoA
show the reaction diagram
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no activity with anaerobically induced enzyme, 15% of the activity relative to benzoate with the aerobically induced enzyme
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ATP + 3-aminobenzoate + CoA
AMP + diphosphate + 3-aminobenzoyl-CoA
show the reaction diagram
3.7% activity in anaerobically grown cells, compared to the activity with benzoate
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?
ATP + 3-chlorobenzoate + CoA
AMP + diphosphate + 3-chlorobenzoyl-CoA
show the reaction diagram
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13% of the activity with benzoate
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?
ATP + 3-fluorobenzoate + CoA
AMP + diphosphate + 3-fluorobenzoyl-CoA
show the reaction diagram
ATP + 3-fluorobenzoate + CoA
AMP + diphosphate + 3-fluorobenzoylCoA
show the reaction diagram
ATP + 3-hydroxybenzoate + CoA
AMP + diphosphate + 3-hydroxybenzoyl-CoA
show the reaction diagram
ATP + 4-aminobenzoate + CoA
AMP + diphosphate + 4-aminobenzoyl-CoA
show the reaction diagram
5.6% activity in anaerobically grown cells, compared to the activity with benzoate
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?
ATP + 4-chlorobenzoate + CoA
AMP + diphosphate + 4-chlorobenzoyl-CoA
show the reaction diagram
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3% of the activity with benzoate
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?
ATP + 4-fluorobenzoate + CoA
AMP + diphosphate + 4-fluorobenzoyl-CoA
show the reaction diagram
ATP + 4-hydroxy-3-methoxybenzoate + CoA
AMP + diphosphate + 4-hydroxy-3-methoxybenzoyl-CoA
show the reaction diagram
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15% of the activity relative to benzoate
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?
ATP + 4-hydroxybenzoate + CoA
AMP + diphosphate + 4-hydroxybenzoyl-CoA
show the reaction diagram
ATP + acetate + CoA
AMP + diphosphate + acetyl-CoA
show the reaction diagram
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?
ATP + benzoate + CoA
?
show the reaction diagram
ATP + benzoate + CoA
AMP + diphosphate + benzoyl-CoA
show the reaction diagram
ATP + cyclohex-1-ene-1-carboxylate + CoA
AMP + diphosphate + cyclohex-1-ene-1-carbonyl-CoA
show the reaction diagram
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8% of the activity relative to benzoate
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?
ATP + cyclohex-1-ene-1-carboxylate + CoA
AMP + diphosphate + cyclohex-1-ene-1-carboxyl-CoA
show the reaction diagram
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13% of the activity with benzoate
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?
ATP + cyclohex-3-ene-1-carboxylate + CoA
AMP + diphosphate + cyclohex-1-ene-1-carboxyl-CoA
show the reaction diagram
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40% of the activity with benzoate
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?
ATP + cyclohexa-1,5-diene-1-carboxylate + CoA
AMP + diphosphate + cyclohexa-1,5-diene-1-carboxyl-CoA
show the reaction diagram
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23% of the activity relative to benzoate
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?
ATP + cyclohexanecarboxylate + CoA
AMP + diphosphate + cyclohexanecarboxyl-CoA
show the reaction diagram
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7% of the activity with benzoate
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?
ATP + DELTA1-cyclohexenecarboxylate + CoA
AMP + diphosphate + DELTA1-cyclohexenecarboxyl-CoA
show the reaction diagram
ATP + DELTA3-cyclohexenecarboxylate + CoA
AMP + diphosphate + DELTA3-cyclohexenecarboxyl-CoA
show the reaction diagram
ATP + glutarate + CoA
AMP + diphosphate + glutaryl-CoA
show the reaction diagram
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?
ATP + isonicotinate + CoA
AMP + diphosphate + isonicotinyl-CoA
show the reaction diagram
ATP + nicotinate + CoA
AMP + diphosphate + nicotinyl-CoA
show the reaction diagram
ATP + phenylacetate + CoA
AMP + diphosphate + phenylacetyl-CoA
show the reaction diagram
ATP + phenylpropionate + CoA
AMP + diphosphate + phenylpropionyl-CoA
show the reaction diagram
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10% of the activity relative to benzoate
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?
ATP + picolinate + CoA
AMP + diphosphate + picolinyl-CoA
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + benzoate + CoA
?
show the reaction diagram
ATP + benzoate + CoA
AMP + diphosphate + benzoyl-CoA
show the reaction diagram
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
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restores activity partially after treatment with EDTA
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,4,5-trichlorophenoxyacetic acid
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concentration dependent inhibitor
2,4-Dichlorophenoxyacetic acid
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concentration dependent inhibitor
2-Hydroxybenzoate
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competitive
5,5'-dithiobis(2-nitrobenzoate)
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benzoyl-CoA
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product inhibition
CoCl2
Anaerobic bacterium
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FeCl2
Anaerobic bacterium
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n-octylglucoside
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weak
NiCl2
Anaerobic bacterium
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p-chloromercuribenzoate
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Tween 100
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.15 - 0.5
2-Aminobenzoate
0.04 - 0.09
2-Fluorobenzoate
0.002 - 0.56
ATP
0.0006 - 0.12
Benzoate
0.089 - 0.18
CoA
0.06 - 0.18
CoASH
0.09 - 0.12
reduced CoA
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
433
Benzoate
Pseudomonas sp.
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additional information
additional information
Pseudomonas sp.
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.016
2-Hydroxybenzoate
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.07
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pH 7.5, 22C
0.081
soluble protein, for benzoyl-CoA synthesis, in 100 mM Tris-HCl (pH 7.8), 10mM KCl, 2.5mM MgCl2, 10mM phospho(enol)-pyruvate, 0.5 mM ATP, 0.25 mM CoA, 0.2mM NADH, 2 units myokinase, 2 units pyruvate kinase, 2U of lactate dehydrogenase, and 0.1 mM substrate
13.4
after 166fold purification, for benzoyl-CoA synthesis, in 100 mM Tris-HCl (pH 7.8), 10 mM KCl, 2.5 mM MgCl2, 10 mM phospho(enol)-pyruvate, 0.5 mM ATP, 0.25 mM CoA, 0.2 mM NADH, 2 units myokinase, 2 units pyruvate kinase, 2 units of lactate dehydrogenase, and 0.1 mM substrate
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.2 - 8.4
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8
Anaerobic bacterium
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.4 - 9.2
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7 - 9
Anaerobic bacterium
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7: about 40% of maximal activity, 9: about 30% of maximal activity
7 - 8.9
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7.0: 10% of maximal activity, 8.0: 75% of maximal activity, 8.4-8.9: maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
Anaerobic bacterium
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22 - 45
Anaerobic bacterium
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22C: about 40% of maximal activity, 45C: about 20% of maximal activity
PDB
SCOP
CATH
ORGANISM
UNIPROT
Burkholderia xenovorans (strain LB400)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
59000
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gel filtration
60000 - 62000
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HPLC gel filtration
60000
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gel filtration
64500
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Comassie blue-stained gel filtration
100000
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gel filtration
120000
126000
gel filtration
130000
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gel filtration, aerobically induced enzyme
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
Anaerobic bacterium
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7 or 8 * 58000, SDS-PAGE
homodimer
monomer
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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acetylation of residue Lys512 inactivates BadA, deacetylation reactivates BadA. Acetyltransferase RpPat modifies BadA, and also modifies acetyl-CoA synthetase. At least two deacetylases reactivate BadAAc. One is SrtN, a sirtuintype NAD+-dependent deacetylase, the other deacetylase is lysine deacetylase LdaA, an acetate-forming protein deacetylase. LdaA reactivates HbaAc and AliAAc in vitro
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
sitting-drop vapor diffusion method at 18 C in 23% PEG 3350 K and 0.2 M sodium formate
Burkholderia xenovorans
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
purified enzyme is insensitive to oxygen
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707
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80C, 1 M imidazole, 500 mM NaCl, 20 mM His/HCl, pH 7.9, 10% glycerol, several months and multiple freeze/thaw cycles
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0C, 1 mg/ml purified enzyme, half-life is 8 days
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in liquid N2, no greater losses of activity after 3-6 months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
at 4C, by a method that includes DEAE-sepharose, source 30Q and reactive green chromatography
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DEAE, anion-exchange, HAP, affinity on reactive red resin and anion-exchange on a Mono-Q chromatography
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DEAE-Toyopearl column chromatography, Phenyl-Sepharose Fast Flow column chromatography, and Superose 12 gel filtration
His-tagged recombinant enzyme
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Ni-NTA resin column chromatography
Burkholderia xenovorans
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expressed in Escherichia coli strain BL21 Star (DE3)
Burkholderia xenovorans
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expression in Escherichia coli
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expression in Streptomyces erythrea of a single additional gene encN from the enterocin pathway allows either production of phenyl-substituted polyketides without medium supplementation, or incorporation of a range of substituted phenyl starter units into such polyketides
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gene bamY, DNA and amino acid sequence comparisons and genotyping
gene xabE, DNA and amino acid sequence determination and analysis, genotyping, regulatory and synthase genes downstream of xabE, overview. Expression in Zea mays plants
overexpression in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
acetylation of residue Lys512 inactivates BadA, deacetylation reactivates BadA
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