A metal‐dependent conformational change provides a structural basis for the inhibition of CTP synthase by gemcitabine‐5′‐triphosphate
Bibliographic record
Abstract
Abstract CTP synthases (CTPS) catalyze the de novo production of CTP using UTP, ATP, and l‐glutamine with the anticancer drug metabolite gemcitabine‐5′‐triphosphate (dF‐dCTP) being one of its most potent nucleotide inhibitors. To delineate the structural origins of this inhibition, we solved the structures of Escherichia coli CTPS (ecCTPS) in complex with CTP (2.0 Å), 2′‐ribo‐F‐dCTP (2.0 Å), 2′‐arabino‐F‐CTP (2.4 Å), dF‐dCTP (2.3 Å), dF‐dCTP and ADP (2.1 Å), and dF‐dCTP and ATP (2.1 Å). These structures revealed that the increased binding affinities observed for inhibitors bearing the 2′‐F‐arabino group (dF‐dCTP and F‐araCTP), relative to CTP and F‐dCTP, arise from interactions between the inhibitor's fluorine atom exploiting a conserved hydrophobic pocket formed by F227 and an interdigitating loop from an adjacent subunit (Q114‐V115‐I116). Intriguingly, crystal structures of ecCTPS•dF‐dCTP complexes in the presence of select monovalent and divalent cations demonstrated that the in crystallo tetrameric assembly of wild‐type ecCTPS was induced into a conformation similar to inhibitory ecCTPS filaments solely through the binding of Na+‐, Mg2+‐, or Mn2+•dF‐dCTP. However, in the presence of potassium, the dF‐dCTP‐bound structure is demetalated and in the low‐affinity, non‐filamentous conformation, like the conformation seen when bound to CTP and the other nucleotide analogues. Additionally, CTP can also induce the filament‐competent conformation linked to high‐affinity dF‐dCTP binding in the presence of high concentrations of Mg2+. This metal‐dependent, compacted CTP pocket conformation therefore furnishes the binding environment responsible for the tight binding of dF‐dCTP and provides insights for further inhibitor design.
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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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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 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".