A shared mechanistic pathway for pyridoxal phosphate–dependent arginine oxidases
Bibliographic record
Abstract
Significance Pyridoxal phosphate (PLP)-dependent enzymes rarely react with oxygen, but an emerging group of oxygen-, PLP-dependent enzymes oxidize l -arginine. Two types of oxidases are known: hydroxylases and desaturases. We demonstrate that arginine desaturases have a minor hydroxylase activity and then show through X-ray crystallographic, mutagenesis, spectroscopic, and computational studies that their mechanism involves two rounds of single-electron transfer to oxygen and superoxide rebound, ultimately giving a conjugated hydroperoxyl intermediate. Water can attack to give a hydroxylated product and release H 2 O 2 , but with water absent, the intermediate can be deprotonated, instead giving a desaturated product and H 2 O 2 . Our work outlines the unique mechanism and evolutionary history of these enzymes and sets the stage toward engineering these enzymes to catalyze oxidative reactions.
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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 | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.003 | 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".