Metal‐Dependent Polysaccharide Deacetylase <scp>PgaB</scp>
Bibliographic record
Abstract
Abstract PgaB is a two‐domain protein responsible for the de‐ N ‐acetylation of poly(β‐1,6‐ N ‐acetyl‐ d ‐glucosamine) ( PNAG ). Many bacteria use deacetylated PNAG ( dPNAG ) as a key extracellular matrix component. De‐ N ‐acetylation is a required modification for polymer export and biofilm formation in Escherichia coli . The N‐terminal domain adopts a (β/α) 7 fold common to the CAZy family‐4 carbohydrate esterases, and exhibits low levels of de‐ N ‐acetylation activity on PNAG oligomers. The de‐ N ‐acetylase active site contains an Asp‐His‐His metal coordination site that can bind various divalent metal cations but has optimal activity with Co 2+ , Ni 2+ , and Fe 2+ . The C‐terminal domain of PgaB adopts a (β/α) 8 fold that is structurally similar to glycoside hydrolases. This domain is proposed to bind PNAG as attempts to display hydrolytic activity have been unsuccessful, but the domain is required for de‐ N ‐acetylation in vivo. Here, we summarize recent advances in the functional characterization of PgaB: the structure, metal specificity, and progress toward inhibitor design.
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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) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".