Structural and kinetic characterization of the Arabidopsis DHQ-SDH: The SDH catalytic mechanism and insights into the modes of substrate channeling and metabolism in the shikimate pathway
Bibliographic record
Abstract
The shikimate pathway (SP) is comprised of seven enzymatic steps and is involved in the biosynthesis of the aromatic amino acids, folates, vitamins, quinones and a variety of other aromatic compounds in bacteria, plants, fungi and apicomplexa parasites. Some of the aromatic compounds are essential for the survival of these organisms; as a result, the shikimate pathway has been an attractive target for the design of antimicrobial and herbicidal agents. The Arabidopsis shikimate pathway enzyme, dehydroquinase-shikimate dehydrogenase (DHQ-SDH) catalyzes the dehydration of dehydroquinate to dehydroshikimate followed by the reduction of dehydroshikimate to shikimate (steps three and four of the SP, respectively). The bifunctional enzyme has been identified in plants and some microbes; however, the majority of microbes encode the monofunctional enzymes. This study is the first to report a crystal structure of a plant shikimate pathway enzyme, DHQ-SDH, in three substrate/ligand bound states: (1) Complex I - DHQ-tartrate-SDH-shikimate, (2) Complex II - DHQ-dehydroshikimate-SDH-shikimate, and (3) Complex III - DHQ-dehydroshikimate/tartrate-SDH-shikimate-NADP(H). The DHQdehydroshikimate-SDH-shikimate complexes reveal a possible mode for substrate transfer between the DHQ and SDH active sites. These findings have provided insight into the mechanism of substrate partitioning at this point in the SP. Moreover, a site-directed mutagenesis approach was taken to investigate the roles of the residues that interact with shikimate at the SDH binding site. Saturation kinetics profiles of these mutants revealed that the conserved Lys 385 and Asp 423 are important for the NADP-dependent oxidation of shikimate, whereas a number of residues are important for the binding and orienting of the substrate for efficient catalysis. This study into the SDH catalytic mechanism has also revealed a possible mode for substrate recognition for the different SDH homologs. Results have indicated that specific sequence motifs found within the SDH substrate binding site may confer substrate specificity in the SDH enzyme family.
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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 | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 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".