Structure and substrate specificity of myo-inositol phosphatases at atomic resolution
Bibliographic record
Abstract
Protein tyrosine phosphatase-like myo-inositol phosphatases (PTPLPs) follow an ordered, sequential dephosphorylation pathway that utilizes the abundant myo-inositol-1,2,3,4,5,6-hexakisphosphate (InsP 6 ) to produce less-phosphorylated myo-inositol phosphates (IPs) containing between one and five phosphoryl groups.To understand PTPLP substrate specificity, I present multiple complex structures of Phytase A from Selenomonas ruminantium (PhyAsr) and Mitsuokella multacida (PhyAmm; a tandem repeat) with various IPs.From these structures I demonstrated that binding of IPs by these enzymes is consistent with a 'lock-and-key' binding mechanism, determined binding differences between InsP 6 and less-phosphorylated IPs, and revised the existing PTPLP substrate specificity model.As part of this work, I have produced the first PhyAmm complex structures and demonstrated that the PhyAmm C-terminal repeat binds substrates using identical phosphoryl binding sites as PhyAsr.Further, I have provided evidence that differential substrate binding in the PhyAmm N-and C-terminal repeats is due to electrostatic differences and a loop insertion causing steric clashes.iii
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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 | 0.001 | 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".