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 (InsP6) 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 InsP6 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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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 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".