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show all sequences of 1.13.11.57

Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6

Sugimoto, K.; Senda, M.; Kasai, D.; Fukuda, M.; Masai, E.; Senda, T.; PLoS ONE 9, e92249 (2014)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
crystallographic analyses of DesB shows that gallate is recognized by several hydrogen bonds. Three groups of the hydrogen bonds recognize a substrate and place the substrate in a productive arrangement
Sphingobium sp. SYK-6
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
the catalytic reaction of the extradiol dioxygenase DesB requires the shift of the Fe(II) ion, leading to the bidentate coordination of the substrate to the Fe(II) ion
Sphingobium sp. SYK-6
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Sphingobium sp. SYK-6
G2IKE5
-
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3,4,5-trihydroxybenzoate + O2
DesB has strict substrate specificity for 3,4,5-trihydroxybenzoate (gallate). Biochemical and structural study show the substrate recognition and catalytic mechanisms of extradiol dioxygenase DesB. Mutational analysis reveals that His124 and His192 in the active site are essential to the catalytic reaction of the extradiol dioxygenase DesB. His124, which interacts with OH(4) of the bound gallate, seems to contribute to proper positioning of the substrate in the active site. His192, which is located close to OH (3) of the gallate, is likely to serve as the catalytic base. Glu377' interacts with OH(5) of the gallate and seems to play a critical role in the substrate specificity
746263
Sphingobium sp. SYK-6
(1E)-4-oxobut-1-ene-1,2,4-tricarboxylate
-
-
-
?
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
30
-
assay at
Sphingobium sp. SYK-6
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Sphingobium sp. SYK-6
Crystallization (Commentary) (protein specific)
Crystallization
Organism
crystallographic analyses of DesB shows that gallate is recognized by several hydrogen bonds. Three groups of the hydrogen bonds recognize a substrate and place the substrate in a productive arrangement
Sphingobium sp. SYK-6
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
the catalytic reaction of the extradiol dioxygenase DesB requires the shift of the Fe(II) ion, leading to the bidentate coordination of the substrate to the Fe(II) ion
Sphingobium sp. SYK-6
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3,4,5-trihydroxybenzoate + O2
DesB has strict substrate specificity for 3,4,5-trihydroxybenzoate (gallate). Biochemical and structural study show the substrate recognition and catalytic mechanisms of extradiol dioxygenase DesB. Mutational analysis reveals that His124 and His192 in the active site are essential to the catalytic reaction of the extradiol dioxygenase DesB. His124, which interacts with OH(4) of the bound gallate, seems to contribute to proper positioning of the substrate in the active site. His192, which is located close to OH (3) of the gallate, is likely to serve as the catalytic base. Glu377' interacts with OH(5) of the gallate and seems to play a critical role in the substrate specificity
746263
Sphingobium sp. SYK-6
(1E)-4-oxobut-1-ene-1,2,4-tricarboxylate
-
-
-
?
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
30
-
assay at
Sphingobium sp. SYK-6
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Sphingobium sp. SYK-6
Other publictions for EC 1.13.11.57
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)
746263
Sugimoto
Molecular mechanism of strict ...
Sphingobium sp. SYK-6
PLoS ONE
9
e92249
2014
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716261
Nogales
Unravelling the gallic acid de ...
Pseudomonas putida, Pseudomonas putida KT 2240
Mol. Microbiol.
79
359-374
2011
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713675
Sugimoto
Crystallization and preliminar ...
Sphingobium sp.
Acta Crystallogr. Sect. F
F65
1171-1174
2009
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715355
Kasai
Characterization of the gallat ...
Sphingomonas paucimobilis, Sphingomonas paucimobilis SYK-6
J. Bacteriol.
187
5067-5074
2005
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715480
Nogales
Molecular characterization of ...
Pseudomonas putida, Pseudomonas putida KT 2240
J. Biol. Chem.
280
35382-35390
2005
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3
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3
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44
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