Mechanistic Analysis of the Unusual Redox-Elimination Sequence Employed by <i>Thermotoga maritima </i>BglT: A 6-Phospho-β-glucosidase from Glycoside Hydrolase Family 4
Bibliographic record
Abstract
"Classical" glycosidases utilize either direct or double-displacement mechanisms involving oxocarbenium ion-like transition states to catalyze the hydrolysis of glycosidic bonds. By contrast, the mechanism of the glycosidases in glycoside hydrolase family 4 has been recently proposed to involve NAD+-mediated redox steps along with alpha,beta-elimination and addition steps via anionic intermediates. Support for this mechanism in BglT, a 6-phospho-beta-glucosidase in family 4, has been provided through mechanistic and X-ray crystallographic analyses [Yip, V. L.Y., et al. (2004) J. Am. Chem. Soc. 126, 8354-8355] in which primary deuterium kinetic isotope effects for the hydride abstraction at C3 and for the alpha-proton abstraction at C2 indicate that these two steps are both partially rate-limiting. Current data reveal that there is no secondary deuterium kinetic isotope effect associated with the rehybridization of the C1 sp3 center to a sp2 center. Furthermore, a flat linear free energy relationship was established with a series of aryl 6-phospho-beta-D-glucosides of varying leaving group abilities. Taken together, these data indicate that cleavage of the C1-O1 linkage does not occur during a rate-limiting step. Since the deprotonation at C2 is slow and partially rate-limiting while the departure of the leaving group is not, a stepwise E1(cb)-type mechanism rather than an E1 or a concerted E2-syn mechanism is proposed. Direct evidence for the role of NAD+ was obtained by reduction in situ using NaBH4 leading to an inactive enzyme that could be reactivated by the addition of excess NAD+. This was accompanied by the expected UV-vis spectrophotometric changes.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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 teacher head, 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".