NAD<sup>+</sup>-dependent RNA terminal 2′ and 3′ phosphomonoesterase activity of a subset of Tpt1 enzymes
Bibliographic record
Abstract
The enzyme Tpt1 removes the 2′-PO 4 at the splice junction generated by fungal tRNA ligase; it does so via a two-step reaction in which (i) the internal RNA 2′-PO 4 attacks NAD + to form an RNA-2′-phospho-ADP-ribosyl intermediate; and (ii) transesterification of the ribose O2″ to the 2′-phosphodiester yields 2′-OH RNA and ADP-ribose-1″,2″-cyclic phosphate products. The role that Tpt1 enzymes play in taxa that have no fungal-type RNA ligase remains obscure. An attractive prospect is that Tpt1 enzymes might catalyze reactions other than internal RNA 2′-PO 4 removal, via their unique NAD + -dependent transferase mechanism. This study extends the repertoire of the Tpt1 enzyme family to include the NAD + -dependent conversion of RNA terminal 2′ and 3′ monophosphate ends to 2′-OH and 3′-OH ends, respectively. The salient finding is that different Tpt1 enzymes vary in their capacity and positional specificity for terminal phosphate removal. Clostridium thermocellum and Aeropyrum pernix Tpt1 proteins are active on 2′-PO 4 and 3′-PO 4 ends, with a 2.4- to 2.6-fold kinetic preference for the 2′-PO 4 . The accumulation of a terminal 3′-phospho-ADP-ribosylated RNA intermediate during the 3′-phosphotransferase reaction suggests that the geometry of the 3′-p-ADPR adduct is not optimal for the ensuing transesterification step. Chaetomium thermophilum Tpt1 acts specifically on a terminal 2′-PO 4 end and not with a 3′-PO 4 . In contrast, Runella slithyformis Tpt1 and human Tpt1 are ineffective in removing either a 2′-PO 4 or 3′-PO 4 end.
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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 | 0.000 | 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".