A Chimeric Variant of Two Gentisate 1,2‐Dioxygenases with Improved Catalytic Activity, Altered Structural Conformation and Substrate Specificity
Bibliographic record
Abstract
Gentisate 1,2‐dioxygenases catalyze the critical ring‐opening step in the metabolism of gentisate (2,5‐dihydroxybenzoate) by microorganisms under aerobic conditions. Gentisate 1,2‐dioxgenases from bacterial species that have been characterized to date are strictly Fe(II)‐dependent and they are mostly homotetrameric in solution. In bacteria, genes coding for gentisate 1,2‐dioxygenase and other enzymes in the rest of the pathway for gentisate degradation are often organized in operons. While genes and enzymes in the gentisate pathway have been relatively well‐studied in bacteria, reports about their fungal counterparts remain scarce in the literature. Here, we report the biochemical characterization of two gentisate 1,2‐dioxygenases from Aspergillus niger with different specific activities that appear to be encoded within two split gene clusters in the A. niger genome. These differences in activities seem to be accompanied by differences in secondary structure and oligomerization states between these two proteins in solution. Furthermore, we report the engineering of a chimeric variant consisting of two domains derived from these two A. niger gentisate 1,2‐dioxgenases that shows improved activity with gentisate, altered structural conformation and substrate specificity able to cleave a substrate that neither of the two wild type gentisate 1,2‐dioxygenases is able to attack.
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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 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| 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".