BRENDA - Enzyme Database
show all sequences of 3.1.1.106

Structural insights into the mechanism of Escherichia coli YmdB A 2-O-acetyl-ADP-ribose deacetylase

Zhang, W.; Wang, C.; Song, Y.; Shao, C.; Zhang, X.; Zang, J.; J. Struct. Biol. 192, 478-486 (2015)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expressed in Escherichia coli Rosetta2 (DE3) cells
Escherichia coli
Crystallization (Commentary)
Crystallization
Organism
sitting drop vapor diffusion method. Wild type enzyme in complex with ADP-D-ribose using 0.2 M potassium sodium tartrate tetrahydrate, 20% w/v polyethylene glycol 3350, double mutant N25A/D35A complexed with 2''-O-acetyl-ADP-D-ribose using 2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, and mutant Y126A in complex with ADP-D-ribose using 2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5
Escherichia coli
Engineering
Amino acid exchange
Commentary
Organism
D35A
the mutant shows strongly reduced activity compared to the wild type enzyme
Escherichia coli
N25A
the mutant shows strongly reduced activity compared to the wild type enzyme
Escherichia coli
N25A/D35A
inactive
Escherichia coli
Y126A
inactive
Escherichia coli
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.4306
-
2''-O-acetyl-ADP-D-ribose
wild type enzyme, at pH 7.5 and 25°C
Escherichia coli
1.358
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme N25A, at pH 7.5 and 25°C
Escherichia coli
2.74
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme D35A, at pH 7.5 and 25°C
Escherichia coli
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2''-O-acetyl-ADP-D-ribose + H2O
Escherichia coli
specific substrate
ADP-D-ribose + acetate
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
P0A8D6
-
-
Purification (Commentary)
Commentary
Organism
Ni-NTA resin column chromatography and Superdex S200 gel filtration
Escherichia coli
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2''-O-acetyl-ADP-D-ribose + H2O
-
751419
Escherichia coli
ADP-D-ribose + acetate
-
-
-
?
2''-O-acetyl-ADP-D-ribose + H2O
specific substrate
751419
Escherichia coli
ADP-D-ribose + acetate
-
-
-
?
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.2
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme D35A, at pH 7.5 and 25°C
Escherichia coli
0.814
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme N25A, at pH 7.5 and 25°C
Escherichia coli
1.31
-
2''-O-acetyl-ADP-D-ribose
wild type enzyme, at pH 7.5 and 25°C
Escherichia coli
Cloned(Commentary) (protein specific)
Commentary
Organism
expressed in Escherichia coli Rosetta2 (DE3) cells
Escherichia coli
Crystallization (Commentary) (protein specific)
Crystallization
Organism
sitting drop vapor diffusion method. Wild type enzyme in complex with ADP-D-ribose using 0.2 M potassium sodium tartrate tetrahydrate, 20% w/v polyethylene glycol 3350, double mutant N25A/D35A complexed with 2''-O-acetyl-ADP-D-ribose using 2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, and mutant Y126A in complex with ADP-D-ribose using 2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5
Escherichia coli
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
D35A
the mutant shows strongly reduced activity compared to the wild type enzyme
Escherichia coli
N25A
the mutant shows strongly reduced activity compared to the wild type enzyme
Escherichia coli
N25A/D35A
inactive
Escherichia coli
Y126A
inactive
Escherichia coli
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.4306
-
2''-O-acetyl-ADP-D-ribose
wild type enzyme, at pH 7.5 and 25°C
Escherichia coli
1.358
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme N25A, at pH 7.5 and 25°C
Escherichia coli
2.74
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme D35A, at pH 7.5 and 25°C
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2''-O-acetyl-ADP-D-ribose + H2O
Escherichia coli
specific substrate
ADP-D-ribose + acetate
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
Ni-NTA resin column chromatography and Superdex S200 gel filtration
Escherichia coli
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2''-O-acetyl-ADP-D-ribose + H2O
-
751419
Escherichia coli
ADP-D-ribose + acetate
-
-
-
?
2''-O-acetyl-ADP-D-ribose + H2O
specific substrate
751419
Escherichia coli
ADP-D-ribose + acetate
-
-
-
?
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.2
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme D35A, at pH 7.5 and 25°C
Escherichia coli
0.814
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme N25A, at pH 7.5 and 25°C
Escherichia coli
1.31
-
2''-O-acetyl-ADP-D-ribose
wild type enzyme, at pH 7.5 and 25°C
Escherichia coli
KCat/KM [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.073
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme D35A, at pH 7.5 and 25°C
Escherichia coli
0.599
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme N25A, at pH 7.5 and 25°C
Escherichia coli
3.042
-
2''-O-acetyl-ADP-D-ribose
wild type enzyme, at pH 7.5 and 25°C
Escherichia coli
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.073
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme D35A, at pH 7.5 and 25°C
Escherichia coli
0.599
-
2''-O-acetyl-ADP-D-ribose
mutant enzyme N25A, at pH 7.5 and 25°C
Escherichia coli
3.042
-
2''-O-acetyl-ADP-D-ribose
wild type enzyme, at pH 7.5 and 25°C
Escherichia coli
Other publictions for EC 3.1.1.106
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)
750645
Agnew
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2
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752262
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-
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1
-
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-
5
-
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3
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2
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1
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3
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1
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4
5
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3
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1
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3
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752189
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Trypanosoma brucei gambiense, Trypanosoma cruzi, Trypanosoma cruzi CL Brener
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6
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2
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9
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2
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9
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2
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2
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9
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2
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9
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751419
Zhang
Structural insights into the ...
Escherichia coli
J. Struct. Biol.
192
478-486
2015
-
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1
1
4
-
-
3
-
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-
1
-
1
-
-
1
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2
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3
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1
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1
4
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3
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1
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1
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2
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3
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3
3
749471
Hirsch
Transition-state analysis of ...
Homo sapiens
ACS Chem. Biol.
9
2255-2262
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1
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2
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2
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2
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2
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2
2
751688
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Homo sapiens
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20
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1
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1
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6
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5
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1
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13
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3
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1
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6
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3
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13
-
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1
3
-
-
-
751029
Chen
Identification of macrodomain ...
Escherichia coli, Homo sapiens, Staphylococcus aureus
J. Biol. Chem.
286
13261-13271
2011
-
-
1
1
15
-
3
4
-
-
-
8
-
8
-
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1
-
-
1
-
-
12
-
-
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18
-
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1
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1
-
1
15
-
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4
1
4
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8
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1
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2
-
-
12
-
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-
18
-
-
-
-
-
-
-
-
4
4
751030
Kasamatsu
Hydrolysis of O-acetyl-ADP-ri ...
Homo sapiens
J. Biol. Chem.
286
21110-21117
2011
-
-
-
-
-
-
4
1
-
1
-
1
-
1
-
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6
1
-
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-
1
-
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3
-
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-
3
4
-
1
-
1
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1
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6
1
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1
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752026
Ono
The 39-kDa poly(ADP-ribose) g ...
Homo sapiens
Proc. Natl. Acad. Sci. USA
103
16687-16691
2006
1
-
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-
3
-
2
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1
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2
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1
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2
1
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1
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1
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3
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2
1
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1
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2
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2
1
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-
751012
Rafty
-
Analysis of O-acetyl-ADP-ribo ...
Homo sapiens, Saccharomyces cerevisiae
J. Biol. Chem.
277
47114-47122
2002
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2
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4
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2
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3
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4
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