Substrate-Assisted Mechanism for the Degradation of N‑Glycans by a Gut Bacterial Mannoside Phosphorylase

• Published in: ACS catalysis Vol. 13; no. 7; pp. 4283 - 4289
• Main Authors: Alfonso-Prieto, Mercedes, Cuxart, Irene, Potocki-Véronèse, Gabrielle, André, Isabelle, Rovira, Carme
• Format: Journal Article
• Language: English
• Published: American Chemical Society 07.04.2023
• Subjects: Biochemistry; Biochemistry, Molecular Biology; Catalysis; Chemical Sciences; Life Sciences; or physical chemistry; Theoretical and; microbiota; mannosides; metadynamics; glycoside phosphorylase; catalytic reaction mechanism; enzyme catalysis; quantum mechanics/molecular mechanics; N-glycans; Microbiota; Enzyme catalysis; Catalytic reaction mechanism; Glycoside phosphorylase
• DOI: 10.1021/acscatal.3c00451
• ISSN: 2155-5435

The unknown human gut bacterium mannoside phosphorylase (UhgbMP) is involved in the metabolization of eukaryotic N-glycans lining the intestinal epithelium, a factor associated with the onset and symptoms of inflammatory bowel diseases. In contrast with most glycoside phosphorylases, the putative catalytic acid of UhgbMP, Asp104, is far from the scissile glycosidic bond, challenging the classical Koshland mechanism. Using quantum mechanics/molecular mechanics metadynamics, we demonstrate that the enzyme operates by substrate-assisted catalysis via the 3-hydroxyl group of the mannosyl unit, following a 1 S 5/B 2,5 → [B 2,5]‡ → 0 S 2 conformational itinerary. Given the conservation of the active site hydrogen bond network across the family, this mechanism is expected to apply to other GH130 enzymes, as well as recently characterized mannoside phosphorylases with similar folds. Gaining insight into the catalytic reaction of these enzymes can aid the design of specific inhibitors to control interactions between gut microbes and the host.