The DHQ-dehydroshikimate-SDH-shikimate-NADP(H) Complex: Insights into Metabolite Transfer in the Shikimate Pathway<sup>,</sup>
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Bibliographic record
Abstract
Plants encode the bifunctional dehydroquinase-shikimate dehydrogenase (DHQ-SDH), which catalyzes the third and fourth steps of the shikimate pathway. We report the Arabidopsis thaliana DHQ-SDH structure in complex with all of its natural substrates. The DHQ-SDH enzyme was first cocrystallized with shikimate. NADP + was subsequently added to the crystals yielding the SDH ternary complex. The Pro-R hydrogen of the nicotinamide C4 is 3.35 Å from the C3 of shikimate, the site of hydride transfer. The catalytic Lys 385 and Asp 423 residues are proximal to the C3-hydroxyl of shikimate, which is deprotonated in the oxidation reaction. The SDH-shikimate-NADP(H) complex represents the active complex as the oxidation of shikimate was evidenced by the generation of the product (dehydroshikimate) found in the DHQ site. DHQ-SDH adopts a concave architecture that places the active sites in a face-to-face arrangement. This proximal organization serves to increase the local effective concentration of dehydroshikimate, and as a consequence, reduces the diffusion of the intermediate to the cellular milieu and competing pathways. Our results have also demonstrated the dependence on a number of residues surrounding the C4-hydroxyl group of shikimate for substrate binding and efficient catalysis, including Thr 407, Thr 422, and Gln 578.
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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 | 0.004 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| 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 it