Bibliographic record
Abstract
Abstract PhnZ is a di‐iron‐dependent monooxygenase from the HD superfamily of metal ion‐dependent phosphohydrolases. These enzymes utilize a conserved histidine‐aspartate motif in the active site for metal ion binding. PhnZ is commonly found in marine bacteria where it works in tandem with the α‐ketoglutarate‐dependent dioxygenase PhnY to extract inorganic phosphate from the organophosphonate natural product 2‐aminoethylphosphonic acid. PhnY hydroxylates 2‐aminoethylphosphonic acid stereospecifically to generate (R)‐2‐amino‐1‐hydroxyethylphosphonic acid, whereupon PhnZ catalyzes the oxidative cleavage of the carbon–phosphorus bond yielding glycine and inorganic phosphate. Analysis of the metal ion dependence of PhnZ through activity assays, ICP‐MS, Mössbauer spectroscopy, and EPR spectroscopy have shown that this enzyme utilizes a mixed‐valence Fe(II)/Fe(III) di‐iron cofactor for catalysis. The X‐ray crystal structures of PhnZ have revealed that one Fe ion (Fe2) is used to bind the substrate in a bidentate manner, while the other Fe ion (Fe1) is likely used to reduce dioxygen. Two conserved active site residues, Y24 and E27, are observed to migrate in and out of the active site in response to substrate binding. Y24 is observed to bind Fe2, occupying the putative dioxygen binding site, but is expelled upon recognition of the substrate amino group by the residue E27. This is proposed to allow dioxygen to bind to Fe1, placing it well within proximity of the substrate bound at Fe2. A mechanism for oxidative carbon–phosphorus bond cleavage by PhnZ has been proposed based on these results. PhnZ not only represents the third known mechanism for enzymatic cleavage of CP‐bonds but also provides a window into the evolution of new functions within an enzyme superfamily.
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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) | 0.003 | 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".