The DHQ-dehydroshikimate-SDH-shikimate-NADP(H) Complex: Insights into Metabolite Transfer in the Shikimate Pathway<sup>,</sup>
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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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 | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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".