- Predicted Function
- Hydrolase enzyme — EC 3, p=1.00. From the sequence, Astra confirms the merely-"probable" deubiquitinase annotation with near-certainty (enzyme, p=0.97).
- Active Site
- Pocket lands on the catalytic dyad. A HIGH-confidence binding pocket (0.90) whose residues include the annotated catalytic Cys456 and His677 — the predicted active site coincides with the (unconfirmed) DUB machinery.
- Fold
- Soluble, cytoplasmic; a large (757 aa), predominantly ordered single chain; no membrane, disorder or amyloid signal.
- Modifications
- A phosphorylation-rich regulatory stretch (~210–290) and predicted ubiquitination — a regulated enzyme.
- Clean Signal
- No disordered or amyloidogenic segments predicted.
Model-reported confidence for the headline calls (amber = the load-bearing prediction the rest of the profile builds on). These are model-estimated probabilities that rank and gate each call — not calibrated rates of experimental success.
The Gap
Why This Target Is Still Dark
MINDY4 (FAM188B) is a protein caught mid-characterisation. UniProt annotates it only as a probable deubiquitinase — a MINDY-family enzyme predicted to cleave Lys48-linked polyubiquitin, with a catalytic dyad (Cys456/His677) inferred but its enzymatic activity and substrates never experimentally confirmed. It has no experimental structure in the PDB and sits at IDG Tdark. Yet it is disease-important and searched: FAM188B is oncogenic in lung cancer, where it deubiquitinates and stabilises the FOXM1 transcription factor and correlates with poor survival; its knockdown sensitises tumour cells to anoikis via EGFR down-regulation and suppresses metastasis.
That combination — a disease-relevant enzyme whose activity is still unproven — is exactly where prediction earns its keep: everything below is computed from the canonical 757-residue sequence and derived structural predictions, with no experimental MINDY4 structure used as input. For an enzyme nobody has confirmed, there is nothing to look up.
Architecture & Topology
How the Sequence Is Organised
| Element | Residues | Note |
|---|---|---|
| N-terminal region | 1–209 | Ordered, soluble; N-terminal to the regulatory and catalytic regions. |
| Phospho-rich stretch | ~210–290 | Dense cluster of predicted phosphosites; a plausible regulatory surface, N-terminal to the catalytic region. |
| Catalytic region | ~420–712 | C-terminal enzyme machinery; contains the annotated catalytic dyad Cys456/His677 and the independently predicted pocket. |
The Predicted Pocket
The Predicted Active Site
The predicted active site is not an extrapolation into empty space: it lands on the two residues UniProt already flags as catalytic. As a control, the same pocket detection recovers the known catalytic/ligand sites on enzymes whose structures are solved, so the MINDY4 active site is a like-for-like prediction rather than a guess — a ranked, testable hypothesis, not a claim of proven activity.
Site: C-terminal catalytic region; the predicted pocket coincides with the annotated catalytic dyad (Cys456, His677)
Post-Translational & Structural Features
Specific, Testable Residues
- Phosphorylation-rich regulatory stretch (~210–290). A dense cluster of predicted phosphosites N-terminal to the catalytic region — a plausible regulatory surface for switching the enzyme on or off, and a starting point for signalling studies.
- Predicted ubiquitination. Consistent with a deubiquitinase that is itself embedded in ubiquitin signalling (auto-regulation or turnover).
- No membrane, disorder or amyloid signal. A clean, soluble, ordered enzyme — the whole chain is a viable target for structural work.
Recommended Experimental Follow-Up
An Orphan Sequence, Turned Into a Ranked Plan
Each prediction is paired with the experiment that would test it and the readout to watch for.
| Prediction | Experiment | Readout |
|---|---|---|
| Hydrolase / deubiquitinase class | In-vitro Ub-chain cleavage assay (K48 di-/poly-Ub) | Confirm (or refute) deubiquitinase activity |
| Catalytic dyad Cys456 / His677 | C456A and H677A active-site mutants | Loss of activity — validates the predicted dyad |
| Predicted pocket residues | Activity-based / covalent-probe labelling | Probe engagement; a starting point for inhibitors |
| FOXM1 as a substrate hypothesis | Ub-chain assay on FOXM1 ± MINDY4 | Change in FOXM1 ubiquitination / stability |
| Phospho-regulatory stretch (~210–290) | Phosphomimetic / phospho-null mutants | Change in DUB activity or FOXM1 / p53 output |
Scope & Limitations
What This Is — and Isn't
- Prediction, not experiment. These are computational hypotheses to prioritise experiments — not a substitute for a structure or an assay. No result here has been validated in the wet lab.
- Function and site are predictions, not assays. Astra confidently calls MINDY4 a hydrolase and places its pocket on the catalytic dyad — but the enzyme's activity has never been confirmed in vitro. These are hypotheses to test, not a demonstration of activity.
- Biology caveats. The oncogenic role rests on knockdown / over-expression studies in cancer cell lines; endogenous substrates beyond FOXM1 are not established. Treat the therapeutic case as a hypothesis.
All predictions were generated with Orbion's Astra suite from the canonical MINDY4 sequence (UniProt Q4G0A6), using AlphaFold-derived structural features. Reported values are model outputs; model internals are out of scope.
References
- [1]UniProt Consortium. UniProtKB entry Q4G0A6 (MINDY4, human). uniprot.org.
- [2]Pharos (Illuminating the Druggable Genome). MINDY4 (FAM188B) target record — Tdark. pharos.nih.gov.
- [3]FAM188B Expression Is Critical for Cell Growth via FOXM1 Regulation in Lung Cancer. Biomedicines 8(11), 465 (2020). https://doi.org/10.3390/biomedicines8110465
- [4]FAM188B Downregulation Sensitizes Lung Cancer Cells to Anoikis via EGFR Down-regulation and Inhibits Tumor Metastasis In Vivo. Cancers 13(2), 247 (2021). https://doi.org/10.3390/cancers13020247