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Literature summary 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

Cloned(Commentary)

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

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.1.1.106 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

EC Number Protein Variants Comment Organism
3.1.1.106 D35A the mutant shows strongly reduced activity compared to the wild type enzyme Escherichia coli
3.1.1.106 N25A the mutant shows strongly reduced activity compared to the wild type enzyme Escherichia coli
3.1.1.106 N25A/D35A inactive Escherichia coli
3.1.1.106 Y126A inactive Escherichia coli

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.1.1.106 0.4306
-
 2''-O-acetyl-ADP-D-ribose wild type enzyme, at pH 7.5 and 25°C Escherichia coli
3.1.1.106 1.358
-
 2''-O-acetyl-ADP-D-ribose mutant enzyme N25A, at pH 7.5 and 25°C Escherichia coli
3.1.1.106 2.74
-
 2''-O-acetyl-ADP-D-ribose mutant enzyme D35A, at pH 7.5 and 25°C Escherichia coli

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.1.1.106 2''-O-acetyl-ADP-D-ribose + H2O Escherichia coli specific substrate ADP-D-ribose + acetate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.1.1.106 Escherichia coli P0A8D6
-
-

Purification (Commentary)

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

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.1.1.106 2''-O-acetyl-ADP-D-ribose + H2O
-
 Escherichia coli ADP-D-ribose + acetate
-
 ?
3.1.1.106 2''-O-acetyl-ADP-D-ribose + H2O specific substrate Escherichia coli ADP-D-ribose + acetate
-
 ?

Synonyms

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

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.1.1.106 0.2
-
 2''-O-acetyl-ADP-D-ribose mutant enzyme D35A, at pH 7.5 and 25°C Escherichia coli
3.1.1.106 0.814
-
 2''-O-acetyl-ADP-D-ribose mutant enzyme N25A, at pH 7.5 and 25°C Escherichia coli
3.1.1.106 1.31
-
 2''-O-acetyl-ADP-D-ribose wild type enzyme, at pH 7.5 and 25°C Escherichia coli

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.1.1.106 0.073
-
 2''-O-acetyl-ADP-D-ribose mutant enzyme D35A, at pH 7.5 and 25°C Escherichia coli
3.1.1.106 0.599
-
 2''-O-acetyl-ADP-D-ribose mutant enzyme N25A, at pH 7.5 and 25°C Escherichia coli
3.1.1.106 3.042
-
 2''-O-acetyl-ADP-D-ribose wild type enzyme, at pH 7.5 and 25°C Escherichia coli