Pyridoxal phosphate‐dependent reactions in natural products biosynthesis
Bibliographic record
Abstract
Pyridoxal 5′‐phosphate (PLP)‐dependent enzymes are widespread in nature. Most reactions catalyzed by PLP‐dependent enzymes traverse through a carbanionic intermediate, which is stabilized by the PLP cofactor. Like all enzymes that deal with carbanions, PLP‐dependent enzymes can be subject to reaction with electrophiles like O 2 . However, the majority reactions of PLP‐dependent enzymes with O 2 are paracatalytic. Recent studies have identified PLP‐dependent enzymes that employ O 2 as a co‐substrate for oxidation of arginine. Such enzymes are part of biosynthetic pathways that convert arginine into heterocycle‐containing natural products. In this talk, I will discuss the discovery of these arginine oxidases, and I will describe what we have learned about their mechanisms. I will furthermore highlight how we characterized an O 2 ‐, PLP‐dependent enzyme encoded by an unknown gene cluster and then used this discovery as a starting point to reconstitute the biosynthetic pathway to the antibiotic azomycin.
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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) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".