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Information on EC 1.13.11.50 - acetylacetone-cleaving enzyme
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1.13.11.50 acetylacetone-cleaving enzymeIUBMB Comments
An Fe(II)-dependent enzyme. Forms the first step in the acetylacetone degradation pathway of Acinetobacter johnsonii. While acetylacetone is by far the best substrate, heptane-3,5-dione, octane-2,4-dione, 2-acetylcyclohexanone and ethyl acetoacetate can also act as substrates.
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Word Map
- 1.13.11.50
-
facial
- acinetobacter
- johnsonii
-
nonheme
- methylglyoxal
-
five-coordinate
-
o2-dependent
-
fe2+-dependent
-
dioxygen-dependent
-
six-coordinate
-
bidentate
-
uv-vis
-
ferrous
-
non-native
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r-groups
-
enzyme-bound
-
enol
-
metal-binding
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2-his-1-carboxylate
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ironii
-
high-spin
- environmental protection
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
diketone cleaving enzyme, acetylacetone dioxygenase, acetylacetone-cleaving enzyme, diketone dioxygenase, diketone-cleaving dioxygenase, diketone cleaving dioxygenase, 
more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
acetylacetone dioxygenase
acetylacetone-cleaving enzyme
b-diketone dioxygenase
-
-
-
-
diketone cleaving dioxygenase
diketone cleaving enzyme
diketone dioxygenase
DKDO
Dke1
oxygenase, b-diketone di-
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-
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acetylacetone dioxygenase
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-
-
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diketone cleaving dioxygenase
-
-
-
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diketone cleaving enzyme
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-
-
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Dke1
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-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
pentane-2,4-dione + O2 = acetate + 2-oxopropanal
-
-
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pentane-2,4-dione + O2 = acetate + 2-oxopropanal
reaction mechanism
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pentane-2,4-dione + O2 = acetate + 2-oxopropanal
first step
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-
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pentane-2,4-dione + O2 = acetate + 2-oxopropanal
An Fe(II)-dependent enzyme. Forms the first step in the acetylacetone degradation pathway of Acinetobacter johnsonii. While acetylacetone is by far the best substrate, heptane-3,5-dione, octane-2,4-dione, 2-acetylcyclohexanone and ethyl acetoacetate can also act as substrates
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
redox reaction
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-
-
-
reduction
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-
-
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oxidation
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-
-
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SYSTEMATIC NAME
IUBMB Comments
acetylacetone:oxygen oxidoreductase
An Fe(II)-dependent enzyme. Forms the first step in the acetylacetone degradation pathway of Acinetobacter johnsonii. While acetylacetone is by far the best substrate, heptane-3,5-dione, octane-2,4-dione, 2-acetylcyclohexanone and ethyl acetoacetate can also act as substrates.
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CAS REGISTRY NUMBER
COMMENTARY
524047-53-8
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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
pentane-2,4-dione + O2
acetate + 2-oxopropanal
-
-
-
-
?
pentane-2,4-dione + O2
acetate + 2-oxopropanal
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i.e. acetylacetone
i.e. acetate and acetone
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?
additional information
?
-
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no substrate: 4-hydroxy-4-methyl-2-pentanone, 3-oxobutanoate, quercetin, catechols, 2,4`-dihydroxyacetophenone, ascorbate
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-
?
additional information
?
-
-
the catalytic reaction proceeds via one common rate-limiting step in the clevage of all substrates accepted by the enzyme
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-
?
additional information
?
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residues Arg80 and Tyr70 promote O2 reduction
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-
?
additional information
?
-
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the enzyme is a mononuclear non-heme iron enzymes, Dke1 active site modelling, overview
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-
?
additional information
?
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acetylacetone dioxygenase catalyzes the dioxygen-dependent degradation of beta-dicarbonyl compounds
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-
?
additional information
?
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Dke1 also performs the atypical cleavage of the alpha-keto acid, 4-hydroxyphenylpyruvate, to form 4-hydroxybenzaldehyde as product instead of the homogentisate product found for 4-hydroxyphenylpyruvate with 4-hydroxyphenylpyruvate dioxygenase, EC 1.13.11.27, analysis of the bonding of the alpha-keto acid, 4-hydroxyphenylpyruvate, to ferrous Dke1 using anaerobic Dke1, added ferrous ammonium sulfate, and 4-hydroxyphenylpyruvate at pH 7.0, overview
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-
?
additional information
?
-
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Ni(II)-complex-adducts show regioselective oxidative cleavage of the aliphatic C-C bond using dioxygen via the substrate activation mechanism without changing the oxidation state of nickel(II) as similar to the wild type enzyme
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-
-
additional information
?
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iron(II) complexes [Fe(L)(CH3CN)3](SO3CF3)2 of tris(2-pyridyl)-based ligands exhibit very similar chemical surroundings to the active site of the enzyme and mimic its functions
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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
additional information
?
-
-
acetylacetone dioxygenase catalyzes the dioxygen-dependent degradation of beta-dicarbonyl compounds
-
-
?
pentane-2,4-dione + O2
acetate + 2-oxopropanal
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-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Iron
Ni2+
Zn2+
additional information
Fe2+
-
0.9-1.0 iron atoms per subunit, bound to active enzyme, essential for catalytic activity
Fe2+
sulfate, necessary for enzyme activity. About 0.9 mol Fe2+/mol wild-type enzyme, less than 5% Fe2+ in mutants except 0.27 mol/mol H104E-enzyme and 0.45 mol/mol H104N-enzyme
Fe2+
Dke1 contains an atypical, three-histidine-ligated, mononuclear non-heme Fe2+ center, spectroscopic analysis, overview. Stabilizing effect of Glu98 on the 6C geometry of the metal center, priming it for substrate ligation. Also Thr107 stabilizes the Fe(II) cofactor
Fe2+
-
the Fe(II) coordinating triad is composed of three His residues, geometric and electronic structure of the Fe(II) center, structure and function comparison with other dioxygenases containing a two histidines and a carboxylate coordinating the iron center in a facial triad, overview
Fe2+
-
active site nonheme monoiron(II) center, facially ligated by three histidine residues, overview. Spectral analysis of Dke1 FeII-alpha-keto acid complexes with 4-hydroxyphneylpyruvate, overview
Fe2+
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nonheme Fe(II) cofactor, distinct organization of the hydrophilic triad in the free and substrate-ligated wild-type enzyme. In the free species, the Fe(II) center is coordinated to three histidines and one glutamate, whereas the substrate-ligated, catalytically competent enzyme-substrate complex has an Fe(II) center with three-histidine coordination, with a small fraction of three-histidine, one-glutamate coordination
Fe2+
-
its active site consists of a redox-active iron(II) center
Iron
-
dependent on, metalloenzyme, 1 iron bound per subunit, required for positioning of the substrate and for rendering of the appropriate electronic environment
Iron
an interplay of residues Glu98, His104, Glu11 (from the neighbor subunit), and Arg80 is the most important for the Fe2+ transport in and out of the protein. The Fe2+ ion when expelled from the binding site can be trapped at different locations within the enzyme. The neighborhood of residue Glu11 (form the neighbor subunit) is the second most favorable binding site for the Fe2+ ion after the active site
additional information
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the enzyme is a mononuclear non-heme iron enzyme, overview
additional information
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spectrophotometrical monitoring, Fe2+ and Fe3+ coordination, formation of iron(II) enzyme-substrate complexes, and detachment kinetics, overview
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Cu2+
20 mM Tris/HCl buffer, pH 7.5, 25°C, 1.2fold molar excess, reversible inactivation of wild-type and mutant enzyme through competition with Fe2+, substrates 200 microM pentane-2,4-dione, 330 microM quercetin, 330 microM potassium oxalate, 330 microM 3,4-dihydroxyphenylacetate
hexacyanoferrate(III)
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2.5 mM, 80% decrease in activity within 10 min
Mn2+
20 mM Tris/HCl buffer, pH 7.5, 25°C, 1.2fold molar excess, reversible inactivation of wild-type and mutant enzyme through competition with Fe2+, substrates 200 microM pentane-2,4-dione, 330 microM quercetin, 330 microM potassium oxalate, 330 microM 3,4-dihydroxyphenylacetate
Ni2+
20 mM Tris/HCl buffer, pH 7.5, 25°C, 1.2fold molar excess, reversible inactivation of wild-type and mutant enzyme through competition with Fe2+, substrates 200 microM pentane-2,4-dione, 330 microM quercetin, 330 microM potassium oxalate, 330 microM 3,4-dihydroxyphenylacetate
Zn2+
20 mM Tris/HCl buffer, pH 7.5, 25°C, 1.2fold molar excess, reversible inactivation of wild-type and mutant enzyme through competition with Fe2+, substrates 200 microM pentane-2,4-dione, 330 microM quercetin, 330 microM potassium oxalate, 330 microM 3,4-dihydroxyphenylacetate
H2O2
1 M H2O2 causes complete loss of enzyme activity in less than 10 min, contains no Fe2+ (probably oxidized to Fe3+), partial reconstitution (40%) with 2 mM Fe2+, 20 mM Tris/HCl buffer, pH 7.5, 25°C
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.006
Pentane-2,4-dione
-
wild type enzyme, using 0.2 mM pentane-2,4-dione in 20 mM Tris/HCl buffer at pH 7.5 and 25°C
0.0065
Pentane-2,4-dione
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mutant enzyme E69Q, using 0.2 mM pentane-2,4-dione in 20 mM Tris/HCl buffer at pH 7.5 and 25°C
additional information
additional information
kinetic first-order rate constants of substrate ligation and steady-state kinetic studies of wild-type and mutant enzymes, overview
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additional information
additional information
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steady-state and single-turnover kinetics of substrate binding and conversion in wild-type Dke1 and mutants, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00043
4,4-difluoro-1-phenyl-1,3-butanedione
-
apparent value at 25°C
0.0043
1,1,1-trifluoro-pentane-2,4-dione
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native enzyme, using 0.09 mM 1,1,1-trifluoro-pentane-2,4-dione in 20 mM Tris/HCl buffer at pH 7.5 and 25°C
0.007
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant Y70A/R80A/E98A
0.033
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant Y70F/R80A/E98A
0.05
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant E98Q
0.074
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant E98A
0.098
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant R80A/E98A
0.1
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant T107A
0.126
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant R80A
0.13
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant Y70A
1.27
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant Y70F
6.6
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant wild-type enzyme
3.6
Pentane-2,4-dione
-
mutant enzyme E69Q, using 0.2 mM pentane-2,4-dione in 20 mM Tris/HCl buffer at pH 7.5 and 25°C
6.6
Pentane-2,4-dione
-
wild type enzyme, using 0.2 mM pentane-2,4-dione in 20 mM Tris/HCl buffer at pH 7.5 and 25°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
as sole carbon source
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
Dke1 also performs the atypical cleavage of the alpha-keto acid, 4-hydroxyphenylpyruvate, to form 4-hydroxybenzaldehyde as product instead of the homogentisate product found for 4-hydroxyphenylpyruvate with 4-hydroxyphenylpyruvate dioxygenase, EC 1.13.11.27, analysis of the bonding of the alpha-keto acid, 4-hydroxyphenylpyruvate, to ferrous Dke1 using anaerobic Dke1, added ferrous ammonium sulfate, and 4-hydroxyphenylpyruvate at pH 7.0, overview. active site was modeling, histidine residues are truncated to methyl imidazole for the model, and constraints imposed by the protein backbone are simulated by fixing the relative positions of the beta-carbons of the backbone. The coordination of the active site is completed with either alpha keto (monoanion) or enolate (dianion) bidentate coordinated 4-hydroxyphenylpyruvate ligand or a monoanionic acetylacetone ligand
additional information
-
Dke1 displays an atypical three-histidine metal binding site. Role of the protein structure in the catalysis of beta-diketone cleavage at the threehistidine metal center of diketone cleaving enzyme by computational methods in correlation with kinetic and mutational analyses. Molecular dynamics simulations, using quantum mechanically deduced parameters for the nonheme Fe(II) cofactor. Distinct organization of the hydrophilic triad in the free and substrate-ligated wild-type enzyme. In the free species, the Fe(II) center is coordinated to three histidines and one glutamate, whereas the substrate-ligated, catalytically competent enzyme-substrate complex has an Fe(II) center with three-histidine coordination, with a small fraction of three-histidine, one-glutamate coordination
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). A0A6J5KC17_9BURK
153
0
16996
TrEMBL
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
16607
18000
66430
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homotetramer
tetramer
homotetramer
-
each subunit is organized in a single-domain beta-barrel fold
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
molecular dynamic simulations with wild-type and mutants E88Q, R80A, Y70A of the Fe2+ free protein, of the enzyme with Fe2+ bound in the active site, without and with applying random force, and of the proteins with the metal ion located at the entrance of the water tunnel
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E69Q
-
lower thermal stability of beta-sheet secondary structure, half catalytic center activity and remarkably silent difference in apparent substrate binding compared to the wild type enzyme
E98Q
F115A
-
site-directed mutagenesis, the mutant shows reduced turnover and altered iron binding compared to the wild-type enzyme
F119A
-
site-directed mutagenesis, the mutant shows reduced turnover and altered iron binding c