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Literature summary for 3.1.1.106 extracted from

  • Zhang, W.; Wang, C.; Song, Y.; Shao, C.; Zhang, X.; Zang, J.
    Structural insights into the mechanism of Escherichia coli YmdB A 2-O-acetyl-ADP-ribose deacetylase (2015), J. Struct. Biol., 192, 478-486 .
    View publication on PubMed
Search for more literature for 3.1.1.106

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli Rosetta2 (DE3) cells Escherichia coli

Crystallization (Commentary)

Crystallization (Comment) 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

Protein Variants

Protein Variants Comment 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 Comment 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 Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2''-O-acetyl-ADP-D-ribose + H2O Escherichia coli specific substrate ADP-D-ribose + acetate
-
 ?

Organism

Organism UniProt Comment Textmining
Escherichia coli P0A8D6
-
-

Purification (Commentary)

Purification (Comment) Organism
Ni-NTA resin column chromatography and Superdex S200 gel filtration Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2''-O-acetyl-ADP-D-ribose + H2O
-
 Escherichia coli ADP-D-ribose + acetate
-
 ?
2''-O-acetyl-ADP-D-ribose + H2O specific substrate Escherichia coli ADP-D-ribose + acetate
-
 ?

Synonyms

Synonyms Comment Organism
O-acetyl-ADP-ribose deacetylase
-
 Escherichia coli
ymdB
-
 Escherichia coli

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment 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 Comment 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