Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary 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)

EC Number Crystallization (Comment) Organism
1.13.11.57 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

EC Number Metals/Ions Comment Organism Structure
1.13.11.57 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

EC Number Organism UniProt Comment Textmining
1.13.11.57 Sphingobium sp. SYK-6 G2IKE5
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.13.11.57 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
-
 ?

Synonyms

EC Number Synonyms Comment Organism
1.13.11.57 DesB
-
 Sphingobium sp. SYK-6

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.13.11.57 30
-
 assay at Sphingobium sp. SYK-6

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.13.11.57 7.5
-
 assay at Sphingobium sp. SYK-6