Metal- and Serine-Dependent Meta-Cleavage Product Hydrolases Utilize Similar Nucleophile-Activation Strategies
Bibliographic record
Abstract
LigY catalyzes the hydrolysis of a meta-cleavage product (MCP), 4,11-dicarboxy-8-hydroxy-9-methoxy-2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (DCHM-HOPDA), in the bacterial catabolism of lignin-derived biphenyl. Most characterized MCP hydrolases are serine-dependent, with hydrolysis proceeding via enol–keto tautomerization followed by an acyl-enzyme intermediate. In contrast, LigY is Zn2+-dependent, with hydrolysis proposed to proceed via tautomerization followed by formation of a gem-diol intermediate. Transient-state kinetic analysis of DCHM-HOPDA turnover revealed the formation of an intermediate possessing a bathochromically shifted spectrum (λmax = 508 nm), similar to that of the ESred intermediate observed during tautomerization in serine-dependent hydrolases. Neither the formation (1/τ1 ≈ 137 s–1) nor the decay (1/τ2 ≈ 23 s–1) of ESred was rate-limiting (kcat = 9.7 ± 0.3 s–1). Furthermore, the rate of ESred decay was 3.4-fold slower in deuterated buffer, suggesting a proton-transfer reaction consist...
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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) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.008 | 0.002 |
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; both teacher heads agree on what is shown here.
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".