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Structural Biology and Analytical Chemistry Approaches for Characterizing C-Glycoside Metabolic Enzymes in Human Gut Microbiota
Published on: May 23, 2025
289
Glycoside-metabolizing oxidoreductase D3dgpA from human gut bacterium
Heji Kim1, Huynh Thi Ngoc Mi1, Joong-Hoon Ahn2
1Metalloenzyme Research Group and Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea.
Frontiers in Bioengineering and Biotechnology
|July 15, 2024
Summary
A novel enzyme, D3dgpA from Dorea sp. MRG-IFC3, oxidizes various C-/O-glycosides, including puerarin. This discovery offers a new pathway for glycoside derivatization.
Area of Science:
- Biochemistry
- Enzymology
- Glycoside Chemistry
Background:
- The Gfo/Idh/MocA family enzyme DgpA previously catalyzed puerarin oxidation.
- The specific enzyme D3dgpA was cloned from the human gut bacterium Dorea sp. MRG-IFC3.
Purpose of the Study:
- To investigate the catalytic activity of D3dgpA on various C-/O-glycosides.
- To elucidate the reaction mechanism and thermodynamic properties of D3dgpA.
- To compare D3dgpA with other glycoside-modifying enzymes.
Main Methods:
- Enzymatic assays using various C-/O-glycosides and methyl β-D-3-oxo-glucopyranoside.
- Density Functional Theory (DFT) calculations for activation energies.
- Comparative analysis of reaction mechanisms.
Main Results:
- D3dgpA catalyzed regiospecific oxidation of C-glycosides to 3"- and 2"-oxo-products.
- D3dgpA facilitated the formation of aglycones and hexose enediolone from O-glycosides.
- DFT calculations revealed low activation energies for isomerization and O-glycosidic bond cleavage.
Conclusions:
- D3dgpA exhibits robust reactivity towards diverse glycosides.
- The enzyme's mechanism differs from Gfo/Idh/MocA and GMC families.
- D3dgpA presents a novel general route for glycoside derivatization.
