ArticlePloS one2014
Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 21 citations in OpenAlex.
- Structural Insights into 4,5-DOPA Extradiol Dioxygenase fromJournal of agricultural and food chemistry · 2025Article
- Development and Application of Whole-Cell Biosensors for the Detection of Gallic Acid.ACS synthetic biology · 2023Article
- Characterization of Protocatechuate 4,5-Dioxygenase fromInternational journal of molecular sciences · 2021Article
- Iron acquisition system of Sphingobium sp. strain SYK-6, a degrader of lignin-derived aromatic compounds.Scientific reports · 2020Article
- Regulation of vanillate and syringate catabolism by a MarR-type transcriptional regulator DesR in Sphingobium sp. SYK-6.Scientific reports · 2019Article
- Isolation of a novel platform bacterium for lignin valorization and its application in glucose-free cis,cis-muconate production.Journal of industrial microbiology & biotechnology · 2019Article
- Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives.The Journal of biological chemistry · 2019Article
- Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition.Journal of visualized experiments : JoVE · 2018Article
- Proteins analysed as virtual knots.Scientific reports · 2017Article
- Crystal structure of the TK2203 protein from Thermococcus kodakarensis, a putative extradiol dioxygenase.Acta crystallographica. Section F, Structural biology communications · 2016Article
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6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DesB, which is derived from Sphingobium sp. SYK-6, is a type II extradiol dioxygenase that catalyzes a ring opening reaction of gallate. While typical extradiol dioxygenases show broad substrate specificity, DesB has strict substrate specificity for gallate. The substrate specificity of DesB seems to be required for the efficient growth of S. sp. SYK-6 using lignin-derived aromatic compounds. Since direct coordination of hydroxyl groups of the substrate to the non-heme iron in the active site is a critical step for the catalytic reaction of the extradiol dioxygenases, the mechanism of the substrate recognition and coordination of DesB was analyzed by biochemical and crystallographic methods. Our study demonstrated that the direct coordination between the non-heme iron and hydroxyl groups of the substrate requires a large shift of the Fe (II) ion in the active site. Mutational analysis revealed that His124 and His192 in the active site are essential to the catalytic reaction of 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. Our biochemical and structural study showed the substrate recognition and catalytic mechanisms of DesB.
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