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Literature summary for 1.13.11.57 extracted from

  • Sugimoto, K.; Senda, M.; Kasai, D.; Fukuda, M.; Masai, E.; Senda, T.
    Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6 (2014), PLoS ONE, 9, e92249 .
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

Crystallization (Comment) 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 Comment 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 UniProt Comment Textmining
Sphingobium sp. SYK-6 G2IKE5
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Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
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 Sphingobium sp. SYK-6 (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate
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Synonyms

Synonyms Comment Organism
DesB
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Sphingobium sp. SYK-6

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
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assay at Sphingobium sp. SYK-6

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
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assay at Sphingobium sp. SYK-6