De-N-acetylation and Export of the Biofilm Exopolysaccharide PNAG
Bibliographic record
Abstract
Bacteria embedded in a self-produced matrix of exopolymeric substances, or biofilm, represent a significant medical problem, as the bacteria are tolerant to antibiotics, protected from the environment, and isolated from the innate immune system. A key component required for the development of the biofilm in a wide variety of pathogenic bacteria is the exopolysaccharide poly-β-1,6-N-acetyl-D-glucosamine (PNAG). Four proteins, PgaA/B/C/D, are required for the polymerization, modification, and export of PNAG in Escherichia coli. PgaB is a two-domain outer membrane lipoprotein essential for the partial de-N-acetylation of PNAG (dPNAG); a process required for polymer export and subsequent biofilm formation. Here we report 1.9 Å and 1.8 Å crystal structures of PgaB and its isolated C-terminal domain in complex with a PNAG hexamer, respectively. Characterization of PgaB de-N-acetylase activity using PNAG oligomers reveals that the enzyme has low catalytic efficiency, and displays length- and metal-dependent de-N-acetylation activity specific for PNAG with preference for Fe 2 + , Ni 2 + , and Co 2 + . Furthermore, tryptophan fluorescence quenching assays show the C-terminal domain binds PNAG oligomers with ~1-4 mM affinity. These data in combination with molecular dynamics simulations of PgaB with N-acetylglucosamine and glucosamine suggest PNAG de-N-acetylation occurs first, with subsequent binding of dPNAG to the C-terminal domain. We propose this concerted action plays a pivotal role in targeting dPNAG for export through the outer membrane porin PgaA.
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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) | 0.000 | 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 | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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".