Redox Mechanism of Glycosidic Bond Hydrolysis Catalyzed by 6-Phospho-α-glucosidase: A DFT Study
Bibliographic record
Abstract
Glycosidic bonds are remarkably resistant to cleavage by chemical hydrolysis. Glycoside hydrolases catalyze their selective hydrolysis in oligosaccharides, polysaccharides, and glycoconjugates by following nonredox catalytic pathways or a net redox-neutral catalytic pathway using NAD(+) and divalent metal ions as cofactors. GlvA (6-phospho-alpha-glucosidase) is a glycosidase belonging to family GH4 and follows a regioselective redox-neutral mechanism of glycosidic-bond hydrolysis that favors alpha- over beta-glycosides. Its proposed catalytic mechanism can be divided into two half-reactions: the first one activates the glucopyranose ring by successively forming intermediates that are oxidized at the 3-, 2-, and 1-positions of the ring, which ultimately facilitate the heterolytic deglycosylation. The second half-reaction is essentially the reverse of the first half-reaction, beginning with the pyranose ring hydroxylation at the anomeric carbon, and it is followed by 3-reduction and regeneration of the active forms of the catalytic site and its cofactors. We investigated the NAD(+)-dependent redox mechanism of glycosidic bond hydrolysis as catalyzed by GlvA through the combined application of density functional theory and a self-consistent reaction field to a large active-site model obtained from the crystallographic structure of the enzyme, then we applied natural bond orbital and second-order perturbation analyses to monitor the electron flow and change in oxidation state on each atomic center along the reaction coordinate to rationalize the energetics and regioselectivity of this catalytic mechanism. We find that in GlvA, the redox catalytic mechanism of hydrolysis is driven by the gradual strengthening of the axial endo-anomeric component within the hexose ring along the reaction coordinate to facilitate the heterolytic dissociation of the axial C1-O bond. In addition, the combined influence of specific components of the generalized anomeric effect fully explains the regioselectivity observed in the catalytic activity of GlvA.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".