ATP‐mediated amino acid recognition by GlnRS
Bibliographic record
Abstract
Glutaminyl‐tRNA synthetase has been a leading model for the study of structure‐function correlations in class I tRNA synthetases. Recognition of the correct amino acid and tRNA by these enzymes is critical for the fidelity of the genetic code. The active site assembly of the quaternary and ternary complexes of GlnRS bound to tRNA Gln , ATP and glutamine, or the aminoacyl‐adenylate analog, QSI, revealed a unique interaction between ATP and glutamine distal to the reactive α‐phosphate and carboxylate moieties: the amide oxygen of glutamine accepts a direct hydrogen bond from the 3′OH group of the ribosyl moiety. Interestingly, the quaternary structure of GlnRS bound to noncognate glutamate shows that the analogous hydrogen bond is not formed. Indeed, examination of all tRNA synthetase crystal structures shows that such a distal contact between ATP and the amino acid R‐group is unique to GlnRS. To elucidate the importance of this interaction two approaches were taken: kinetic analysis using an ATP analog, 3′dATP, and crystallization of GlnRS bound to the noncognate aminoacyl‐adenylate analog, glutamol‐AMP. The kinetic findings demonstrate the importance of the unique hydrogen bond: while the Km of 3′‐dATP for GlnRS is unaltered, kcat/Km is decreased by 10 3 fold, and the affinity for glutamine is weakened by 20‐fold. The crystal structure of the noncognate ternary complex confirms that the distal interaction is unique to glutamine binding. Funded by NIH.
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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 | 0.001 |
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".