Catalytic promiscuity and mechanistic determinants of ODCase – a high-resolution investigation
Bibliographic record
Abstract
as problem to be solved. We determined a crystal structure of a complex of ArgRS from Pyrococcus horikoshii, tRNA Arg CCU and ATP analog with Rfactor = 0.215 (Rfree = 0.259) at 2.0 resolution and could give one solution for this problem using newly obtained structural information about position of ATP. The experimental results show that the ArgRS protein lacking the additional N-terminal domain characteristic for ArgRS possesses sufficient catalytic activity in the aminoacylation reaction for tRNA. Modeling of relative positions of amino acid, Ade76 of tRNA and ATP on ArgRS was made to find the suitable position to tRNA-assisted formation mechanism of Arg-AMP. It was found that formation of hydrogen bond between 2'OH of Ade76 of tRNA and O2 of carboxy group -C-O2H=O1 of arginine can be achieved in one conformation by rotation around C -C of carboxy group. In ATP-PPi exchange reaction at low pH, reversible conversion between C=O1 and C-O1-P is controlled by the formation of this hydrogen bond. On the other hand, at pH8.0, experimental results in the deacylation reaction of Arg-tRNA is also understood by mechanism that NH + of guanidium group -N + H=C-(NH2)2 of Arg-tRNA donates a proton to C=O2 of ester bond of Arg-tRNA, resulting in carbonium C + -O2H. We discuss in detail these mechanisms.
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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) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| 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".