BRENDA - Enzyme Database show
show all sequences of 1.13.11.50

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

Brkic, H.; Buongiorno, D.; Ramek, M.; Straganz, G.; Tomic, S.; J. Biol. Inorg. Chem. 17, 801-815 (2012)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expression of Strep-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
Acinetobacter johnsonii
Engineering
Amino acid exchange
Commentary
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
Commentary
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
Commentary
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
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
pentane-2,4-dione + O2
Acinetobacter johnsonii
-
acetate + methylglyoxal
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Acinetobacter johnsonii
-
-
-
Purification (Commentary)
Commentary
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
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1,1-difluoropentane-2,4-dione + O2
-
725553
Acinetobacter johnsonii
?
-
-
-
?
pentane-2,4-dione + O2
-
725553
Acinetobacter johnsonii
acetate + methylglyoxal
-
-
-
?
Subunits
Subunits
Commentary
Organism
homotetramer
each subunit is organized in a single-domain beta-barrel fold
Acinetobacter johnsonii
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Acinetobacter johnsonii
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
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
Commentary
Organism
7.5
-
assay at
Acinetobacter johnsonii
Cloned(Commentary) (protein specific)
Commentary
Organism
expression of Strep-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
Acinetobacter johnsonii
Engineering (protein specific)
Amino acid exchange
Commentary
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] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
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 (protein specific)
Metals/Ions
Commentary
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) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
pentane-2,4-dione + O2
Acinetobacter johnsonii
-
acetate + methylglyoxal
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant Strep-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by affinity chromatography
Acinetobacter johnsonii
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1,1-difluoropentane-2,4-dione + O2
-
725553
Acinetobacter johnsonii
?
-
-
-
?
pentane-2,4-dione + O2
-
725553
Acinetobacter johnsonii
acetate + methylglyoxal
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
homotetramer
each subunit is organized in a single-domain beta-barrel fold
Acinetobacter johnsonii
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Acinetobacter johnsonii
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
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 (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Acinetobacter johnsonii
General Information
General Information
Commentary
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
General Information (protein specific)
General Information
Commentary
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
Other publictions for EC 1.13.11.50
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
742322
Brkic
-
Insight of the iron binding a ...
Acinetobacter johnsonii
Croat. Chem. Acta
88
297-306
2015
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725553
Brkic
Dke1--structure, dynamics, and ...
Acinetobacter johnsonii
J. Biol. Inorg. Chem.
17
801-815
2012
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1
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4
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1
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2
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725198
Diebold
Spectroscopic and computationa ...
Acinetobacter johnsonii
J. Am. Chem. Soc.
133
15979-15991
2011
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1
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711258
Diebold
The three-his triad in Dke1: c ...
Acinetobacter johnsonii
Biochemistry
49
6945-6952
2010
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711267
Straganz
Kinetic and CD/MCD spectroscop ...
Acinetobacter johnsonii
Biochemistry
49
996-1004
2010
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9
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1
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1
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1
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3
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9
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1
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696107
Leitgeb
Biochemical characterization a ...
Acinetobacter johnsonii
Biochem. J.
418
403-411
2009
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1
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8
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6
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1
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1
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8
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6
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675466
Straganz
-
Exploring the cupin-type metal ...
Acinetobacter johnsonii
J. Mol. Catal. B
39
171-178
2006
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657614
Hofer
Fast determination of operatio ...
Acinetobacter johnsonii
Appl. Microbiol. Biotechnol.
1
1-12
2005
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1
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657866
Grogan
Emergent mechanistic diversity ...
Acinetobacter johnsonii
Biochem. J.
388
721-730
2005
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1
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671683
Straganz
-
Integrated approach for produc ...
Acinetobacter johnsonii
Biocatal. Biotransform.
23
261-269
2005
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674150
Straganz
Reaction coordinate analysis f ...
Acinetobacter johnsonii
J. Am. Chem. Soc.
127
12306-12314
2005
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4
1
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4
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636327
Straganz
Acetylacetone-cleaving enzyme ...
Acinetobacter johnsonii
Biochem. J.
369
573-581
2003
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1
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5
1
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1
1
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11
1
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5
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11
1
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1
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636328
Straganz
A novel beta-diketone-cleaving ...
Acinetobacter johnsonii
Biochem. Biophys. Res. Commun.
297
232-236
2002
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