Distinct Role of Specific Tryptophans in Facilitating Electron Transfer or as [Fe(IV)=O Trp<sup>•</sup>] Intermediates in the Peroxidase Reaction of Bulkholderia pseudomallei Catalase-Peroxidase: A Multifrequency EPR Spectroscopy Investigation
Bibliographic record
Abstract
We have characterized the reactive intermediates of the peroxidase-like reaction of Bulkholderia pseudomallei KatG using multifrequency EPR spectroscopy. The aim was to investigate the putative role of tryptophanyl radicals as alternative intermediates to the [Fe(IV)=O Por(*+)] species or as short-lived species involved in superexchange-coupled pathways between redox cofactors. Three distinct sites for the formation of radical intermediates, Trp330, Trp139 and Trp153, were identified using single, double and triple variants of Bulkholderia pseudomallei KatG. The proximal Trp330 is the site for a radical in magnetic interaction with the ferryl heme iron [Fe(IV)=O Trp(*+)], formed at the expense of a short-lived [Fe(IV)=O Por(*+)] species as in the cases of Mycobacterium tuberculosis KatG and cytochrome c peroxidase. Formation of the Trp153 radical at a site close to the enzyme surface crucially depends on the integrity of the H-bonding network of the heme distal side, that includes Trp95, the radical site in the Synechocystis KatG. Accordingly, the extended H-bonding network and Trp94 provide an electron transfer pathway between Trp153 and the heme. The distal tryptophan (Trp111) being part of the KatG-specific adduct required for the catalase-like activity, is involved in facilitating electron transfer for the formation of the Trp139 radical. We propose a comprehensive description of the role of specific Trp residues that takes into account not only the apparent differences in sites for the Trp(*) intermediates in other catalase-peroxidases but also the similar cases observed in monofunctional peroxidases.
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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".