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Literature summary for 1.13.11.50 extracted from

  • Brkic, H.; Buongiorno, D.; Ramek, M.; Straganz, G.; Tomic, S.
    Dke1--structure, dynamics, and function: a theoretical and experimental study elucidating the role of the binding site shape and the hydrogen-bonding network in catalysis (2012), J. Biol. Inorg. Chem., 17, 801-815.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
expression of Strep-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) Acinetobacter johnsonii

Protein Variants

Protein Variants Comment Organism
F115A site-directed mutagenesis, the mutant shows reduced turnover and altered iron binding compared to the wild-type enzyme Acinetobacter johnsonii
F119A site-directed mutagenesis, the mutant shows reduced turnover and altered iron binding compared to the wild-type enzyme Acinetobacter johnsonii
F59A site-directed mutagenesis, the mutant shows reduced turnover and altered iron binding compared to the wild-type enzyme Acinetobacter johnsonii
Y70F site-directed mutagenesis, the mutant shows reduced turnover and altered iron binding compared to the wild-type enzyme Acinetobacter johnsonii

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information steady-state and single-turnover kinetics of substrate binding and conversion in wild-type Dke1 and mutants, overview Acinetobacter johnsonii

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ 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 Acinetobacter johnsonii
additional information spectrophotometrical monitoring, Fe2+ and Fe3+ coordination, formation of iron(II) enzyme-substrate complexes, and detachment kinetics, overview Acinetobacter johnsonii

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
pentane-2,4-dione + O2 Acinetobacter johnsonii
-
acetate + methylglyoxal
-
?

Organism

Organism UniProt Comment Textmining
Acinetobacter johnsonii
-
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant Strep-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by affinity chromatography Acinetobacter johnsonii

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1,1-difluoropentane-2,4-dione + O2
-
Acinetobacter johnsonii ?
-
?
pentane-2,4-dione + O2
-
Acinetobacter johnsonii acetate + methylglyoxal
-
?

Subunits

Subunits Comment Organism
homotetramer each subunit is organized in a single-domain beta-barrel fold Acinetobacter johnsonii

Synonyms

Synonyms Comment Organism
diketone cleaving enzyme
-
Acinetobacter johnsonii
Dke1
-
Acinetobacter johnsonii

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
assay at Acinetobacter johnsonii

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0015
-
1,1-difluoropentane-2,4-dione mutant Y70F, pH 7.5, 25°C Acinetobacter johnsonii
0.008
-
1,1-difluoropentane-2,4-dione mutant F59A, pH 7.5, 25°C Acinetobacter johnsonii
0.018
-
1,1-difluoropentane-2,4-dione mutant F115A, pH 7.5, 25°C Acinetobacter johnsonii
0.022
-
1,1-difluoropentane-2,4-dione mutant F119A, pH 7.5, 25°C Acinetobacter johnsonii
0.036
-
1,1-difluoropentane-2,4-dione wild-type enzyme, pH 7.5, 25°C Acinetobacter johnsonii
0.7
-
Pentane-2,4-dione mutant F59A, pH 7.5, 25°C Acinetobacter johnsonii
1.27
-
Pentane-2,4-dione mutant Y70F, pH 7.5, 25°C Acinetobacter johnsonii
1.4
-
Pentane-2,4-dione mutant F115A, pH 7.5, 25°C Acinetobacter johnsonii
3.2
-
Pentane-2,4-dione mutant F119A, pH 7.5, 25°C Acinetobacter johnsonii
6.6
-
Pentane-2,4-dione wild-type enzyme, pH 7.5, 25°C Acinetobacter johnsonii

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
assay at Acinetobacter johnsonii

General Information

General Information Comment Organism
evolution the enzyme belongs to the cupin superfamily of proteins Acinetobacter johnsonii
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 Acinetobacter johnsonii