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 Fe2+, Ni2+, and Co2+. 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 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) | 0.000 | 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) | 0.001 | 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 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".