mmf2 is a fission-yeast member of the RidA/YjgF/YER057c/UK114 (Rid) family of reactive enamine/imine deaminases ("metabolite-damage pre-emption" enzymes). Proteins of this family form homotrimers and use a single conserved active-site arginine to hydrolyze reactive enamine/imine intermediates - most characteristically 2-aminoacrylate and the corresponding imines 2-iminopropanoate and 2-iminobutanoate, produced by pyridoxal-5'-phosphate-dependent serine/threonine dehydratases - to the stable 2-oxo (keto) acids, thereby protecting PLP-dependent enzymes from covalent damage. mmf2 carries an N-terminal mitochondrial targeting sequence and is assigned to the mitochondrial matrix, with a portion also detected in the cytoplasm. Its characterized Saccharomyces cerevisiae paralog Mmf1p acts in the mitochondrion, where deaminase activity indirectly supports mitochondrial genome integrity by preventing 2-aminoacrylate stress arising from mitochondrial amino-acid catabolism; human UK114/HRSP12 has been reported in several cellular compartments rather than having a settled mitochondrial location. S. pombe also encodes the closely related paralog Pmf1p/mmf1, and the functional and subcellular division of labor between these two fission-yeast Rid proteins remains unresolved. The specific in-vivo substrate, localization, and physiological role of mmf2 have not been experimentally defined.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0019239 deaminase activity | IBA GO_REF:0000033 | MODIFY | Summary: RidA/Rid-family molecular function. Deaminase activity is domain-defensible: mmf2 belongs to PANTHER PTHR11803 (2-iminobutanoate/2-iminopropanoate deaminase RidA) and retains the single conserved catalytic arginine essential for imine/enamine hydrolysis. The term is correct but very general; a more specific RidA term (GO:0120241) better captures the activity and is proposed in core_functions. Reason: The IBA-supported family activity is real, but "deaminase activity" is uninformatively broad for a RidA protein. The specific RidA reaction is 2-iminobutanoate/2-iminopropanoate (and 2-aminoacrylate) deamination. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000211014 · RidA/Rid family ancestral node (PTHR11803) IBA seed node annotated with the generic ancestral term "deaminase activity" rather than the specific RidA reaction, so the transfer to mmf2 is imprecise. UniProtKB:P0AF93 · E. coli RidA SUPPORTS TRANSFER Canonical RidA with direct experimental deaminase evidence; its presence among the descendant evidence supports refinement to GO:0120241. Proposed replacements: 2-iminobutanoate/2-iminopropanoate deaminase activity Supporting Evidence: PMID:25975565 The Rid1, Rid2, and Rid3 subfamilies retain the conserved arginine and glutamate residues found in RidA |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: Mitochondrial localization is well supported: mmf2 has a predicted N-terminal mitochondrial transit peptide and its characterized orthologs act in the mitochondrion. This is the general (organelle-level) term; mitochondrial matrix (GO:0005759) is the more precise location. Reason: Consistent with the transit peptide and with ISO-supported mitochondrial-matrix localization; correct but less precise than the matrix term. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Cytosolic localization has positive support: UniProt assigns Q9UR06 to both cytoplasm and mitochondrion, most eukaryotic RidA proteins are cytosolic, and the cytosol IBA comes from PTN000211014, a different PAINT node from the mitochondrial IBA (PTN008330222). It may represent a genuine second pool rather than only pre-import protein. Reason: Retained as a plausible secondary location supported by deliberate PAINT node placement and the dual UniProt assignment. The transit peptide and ISO matrix annotation currently make the mitochondrial matrix the leading core location, but direct mmf2 localization is needed. Supporting Evidence: PMID:32576850 In most eukaryotes, RidA is a cytosolic enzyme encoded by a single-copy gene. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Electronic mapping from the UniProt Cytoplasm subcellular-location keyword (SL-0086). Broad parent of cytosol; consistent with a non-mitochondrial pool but not the core site. Reason: General cytoplasmic term derived from the UniProt SubCell keyword; retained as non-core, subsumed by the more specific cytosol annotation. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic mapping from the UniProt Mitochondrion subcellular-location keyword (SL-0173), consistent with the predicted transit peptide and the ISO matrix annotation. Reason: Localization is well supported by the transit peptide and orthology; the term is correct though less precise than mitochondrial matrix. |
| GO:0008150 biological_process | ND GO_REF:0000015 | KEEP AS NON CORE | Summary: Root biological_process placeholder with ND evidence, indicating no experimentally or phylogenetically curated BP is assigned in fission yeast. This reflects the genuine BP knowledge gap for this "conserved unknown" gene (see knowledge_gaps). Reason: ND root placeholder; retained as-is. It correctly signals that no specific biological process has been established for the fission-yeast protein. |
| GO:0005759 mitochondrial matrix | ISO GO_REF:0000024 | ACCEPT | Summary: Best-supported subcellular location: transferred by orthology (ISO) from S. cerevisiae Mmf1p, a characterized mitochondrial-matrix factor, and consistent with mmf2's predicted mitochondrial transit peptide. Reason: Precise, orthology-supported localization consistent with the transit-peptide prediction; the primary/core location for this protein. Supporting Evidence: PMID:11003673 Mmf1p is a mitochondrial matrix |
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Download this section (compressed HTML)Q: Does fission-yeast mmf2 hydrolyze 2-aminoacrylate / 2-iminopropanoate in vitro, and is Arg101 the essential catalytic residue?
Q: Does deletion of mmf2 in S. pombe cause mitochondrial DNA loss / a respiratory (petite) phenotype or serine/2-aminoacrylate sensitivity, as seen for S. cerevisiae Mmf1p?
Q: Does the PAINT/PANTHER gene tree place mmf2 with mitochondrial Mmf1p or cytosolic Hmf1p, and how should that placement affect the matrix ISO and cytosol IBA annotations?
Experiment: Purify recombinant mmf2 (mature form) and an Arg101->Ala variant; assay deamination of 2-aminoacrylate and 2-iminobutanoate using coupled serine/threonine-dehydratase pyruvate/2-oxobutanoate production assays, comparing rates to S. enterica RidA and S. cerevisiae Mmf1p.
Hypothesis: mmf2 is a mitochondrial RidA deaminase that hydrolyzes 2-aminoacrylate/2-iminopropanoate via its conserved catalytic arginine.
Type: in vitro enzyme assay
Experiment: Construct an mmf2 deletion, quantify mitochondrial DNA content and respiratory competence, test sensitivity to serine and to conditions that elevate mitochondrial serine/threonine dehydratase flux, and test complementation by S. cerevisiae MMF1 or human HRSP12/UK114.
Hypothesis: mmf2 protects the fission-yeast mitochondrial genome against 2-aminoacrylate stress.
Type: genetics / mitochondrial phenotyping
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