Characterization of an extradiol dioxygenase involved in the catabolism of lignin‐derived biphenyl
Bibliographic record
Abstract
In the catabolism of lignin‐derived biphenyl by Sphingobium sp. SYK‐6, LigZ catalyzes the cleavage of 2,2′,3‐trihydroxy‐3′‐methoxy‐5,5′‐dicarboxybiphenyl (OH‐DDVA) to a meta ‐cleavage product (MCP) identified here as 4,11‐dicarboxy‐8‐hydroxy‐9‐methoxy‐2‐hydroxy‐6‐oxo‐6‐phenylhexa‐2,4‐dienoate (DCHM‐HOPDA). DCHM‐HOPDA is transformed nonenzymatically, likely to a lactone ( k = 0.13 ± 0.01 min −1 , pH 7.5). This is hydrolyzed to the dienolate at alkaline pH (apparent p K a ~ 11.3). Only the dienolate is a substrate for LigY, the putative MCP hydrolase. LigZ has higher specificity for OH‐DDVA ( k cat / K m = 2.20 ± 0.02 × 10 7 s −1 · m −1 ) than for protocatechuate (PCA; 6 ± 1 × 10 2 s −1 · m −1 ). PCA also inactivates LigZ (partition ratio of 50), but at rates too low to be physiologically relevant. This study provides insight into the bacterial catabolism of lignin and facilitates the study of downstream catabolic enzymes.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| 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) | 0.000 | 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 teacher head, 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".