Biochemical, structural, and kinetic characterization of <scp>PP<sub>i</sub></scp>‐dependent phosphoenolpyruvate carboxykinase from <i>Propionibacterium freudenreichii</i>
Bibliographic record
Abstract
Abstract Phosphoenolpyruvate carboxykinases (PEPCK) are a well‐studied family of enzymes responsible for the regulation of TCA cycle flux, where they catalyze the interconversion of oxaloacetic acid (OAA) and phosphoenolpyruvate (PEP) using a phosphoryl donor/acceptor. These enzymes have typically been divided into two nucleotide‐dependent classes, those that use ATP and those that use GTP. In the 1960's and early 1970's, a group of papers detailed biochemical properties of an enzyme named phosphoenolpyruvate carboxytransphosphorylase (later identified as a third PEPCK) from Propionibacterium freudenreichii ( PP i ‐ Pf PEPCK), which instead of using a nucleotide, utilized PP i to catalyze the same interconversion of OAA and PEP. The presented work expands upon the initial biochemical experiments for PP i ‐ Pf PEPCK and interprets these data considering both the current understanding of nucleotide‐dependent PEPCKs and is supplemented with a new crystal structure of PP i ‐ Pf PEPCK in complex with malate at a putative allosteric site. Most interesting, the data are consistent with PP i ‐ Pf PEPCK being a Fe 2+ activated enzyme in contrast with the Mn 2+ activated nucleotide‐dependent enzymes which in part results in some unique kinetic properties for the enzyme when compared to the more widely distributed GTP‐ and ATP‐dependent enzymes.
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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 | 0.001 |
| 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".