mmf2 (SPAC1039.10) — S. pombe — curation notes

Identity / provenance

• UniProt: Q9UR06 (MMF2_SCHPO), 126 aa precursor, "Protein mmf2, mitochondrial";
  AltName "Maintenance of mitochondrial function 2". PomBase standard name mmf2,
  systematic name SPAC1039.10 (synonym hpm1; obsolete ORF SPAC922.01).
  [genes/SCHPO/mmf2/mmf2-uniprot.txt]
• PomBase product line: "mitochondrial matrix protein, YjgF family protein Mmf2,
  reactive intermediate imine deaminase A homolog, NNf2, implicated in detoxification
  and branched amino acid biosynthesis"; characterisation status = "conserved unknown"
  (queried PomBase JSON API 2026-07-06). So there is no direct experimental
  characterisation of the pombe protein's biochemical activity; the annotations are
  homology/phylogeny-based.

Domain / family (inline domain reasoning)

• Family: RidA / YjgF / YER057c / UK114 (a.k.a. RutC family). UniProt SIMILARITY:
  "Belongs to the RutC family." InterPro IPR006056 (RidA), IPR006175
  (YjgF/YER057c/UK114), IPR035959 (RutC-like_sf); Pfam PF01042 (Ribonuc_L-PSP);
  CDD cd00448 (YjgF_YER057c_UK114_family); NCBIfam TIGR00004 "Rid family detoxifying
  hydrolase"; PANTHER PTHR11803 "2-IMINOBUTANOATE/2-IMINOPROPANOATE DEAMINASE RIDA",
  subfamily PTHR11803:SF58 "PROTEIN HMF1-RELATED". [mmf2-uniprot.txt]
• These proteins form homotrimers with three active-site clefts at the subunit
  interfaces (canonical RidA fold; Gene3D 3.30.1330.40 RutC-like).
• Catalytic-residue check (done inline). RidA imine/enamine deaminase activity
  requires a single conserved active-site arginine (Arg105 in S. enterica RidA;
  Arg107 in human hp14.5) that makes a bidentate salt bridge to the substrate
  carboxylate. I aligned mmf2 (Q9UR06) to S. enterica RidA by pairwise global
  alignment (script run under uv/python 3.12). mmf2 retains:
• the catalytic Arg in the conserved C-terminal P-A-R motif: mmf2 ...DPMPAR...
  R at position 101 aligns to RidA ...NATFPAR... R105.
• the conserved N-terminal G-P-Y substrate-pocket motif (mmf2 pos 15 GGPY,
  RidA pos 15 GPY).
• the conserved C-terminal KIEIE motif (mmf2 pos 117, RidA pos 118).
  => The catalytic machinery for imine/enamine (2-iminopropanoate / 2-iminobutanoate /
  2-aminoacrylate) deamination is intact. A RidA-type deaminase MF is therefore
  domain-defensible for mmf2.

What is KNOWN (well-supported)

1. RidA-family enamine/imine deaminase activity (by orthology + conserved catalytic Arg).
   RidA proteins hydrolyze the reactive enamine 2-aminoacrylate (2AA) and related
   enamines/imines (e.g. 2-iminopropanoate/2-iminobutanoate) to the corresponding
   2-oxo (keto) acids, pre-empting metabolite damage.
   PMID:29487232
   PMID:25975565
   Direct work on human RIDA confirms that a eukaryotic ortholog deaminates reactive
   enamine-imine intermediates PMID:33916919.
   A duplicated salmon RidA pair retained imine-deaminase activity but diverged in
   substrate preference PMID:32576850, supporting the activity class while preserving the mmf2 substrate-specificity caveat.
2. Mitochondrial (matrix) localization — UniProt has a predicted N-terminal
   mitochondrial transit peptide (Flags: Precursor; KW Transit peptide) and
   SUBCELLULAR LOCATION Mitochondrion + Cytoplasm. PomBase/GOA: mitochondrial matrix
   (ISO from S. cerevisiae Mmf1p, SGD:S000001313) and cytosol/mitochondrion (IBA).
   [mmf2-uniprot.txt]
3. Ortholog function (S. cerevisiae Mmf1p / YIL051C) — the source of the "Mmf" name.
   Mmf1p is a mitochondrial-matrix RidA protein; deletion causes loss of mtDNA and a
   growth defect (Δmmf1 → rho0 petite). The paralog Hmf1p (cytoplasmic) has no visible
   deletion phenotype but can functionally replace Mmf1p when routed to mitochondria.
   [PMID:11003673 "Mmf1p is a mitochondrial matrix factor" ... "Deltammf1 cells lose mitochondrial DNA (mtDNA) and have a decreased growth rate, while Deltahmf1 cells do not display any visible phenotype"]
   Mechanistically, Mmf1p maintains mtDNA indirectly by deaminating 2AA generated
   by mitochondrial PLP-dependent serine/threonine dehydratases (Ilv1p, Cha1p); without
   Mmf1p, 2AA accumulates and damages PLP enzymes (incl. iron-metabolism enzymes),
   destabilizing the mitochondrial genome. Human UK114 can substitute for Mmf1p.
   PMID:29487232
   PMID:29487232

What is NOT known (gaps specific to pombe mmf2)

• No direct biochemistry on the pombe protein: the specific in-vivo enamine/imine
  substrate for mmf2 (2-aminoacrylate vs 2-iminobutanoate vs a broader set) has not
  been demonstrated experimentally. Family assignment (PANTHER SF58 "HMF1-RELATED")
  and the intact catalytic Arg make 2AA/2-iminopropanoate the most likely substrate,
  but this is inference.
• No characterized mmf2Δ phenotype in pombe tied to mtDNA/2AA. PomBase records
  only high-throughput screen phenotypes (deletion is viable, normal morphology;
  scattered stress sensitivities: diamide, lithium/LiCl, tunicamycin, terbinafine,
  itraconazole, KCl/MgCl2/LiCl+SDS; resistance to EGTA; decreased centromeric outer-repeat
  silencing). None of these was individually followed up, and none directly demonstrates
  a 2AA / mtDNA-maintenance role in pombe. (PomBase single-locus phenotype list,
  queried 2026-07-06.)
• Mitochondrial-matrix localization is inferred, not directly shown in pombe
  (ISO from cerevisiae + transit-peptide prediction). The dual mito/cytoplasm
  annotation may reflect a fraction in the cytosol (as for the cerevisiae paralog Hmf1p)
  or simply pre-import protein; not experimentally resolved for pombe.
• Paralog boundary: S. pombe encodes Pmf1p/mmf1 and Hpm1p/mmf2. PMID:12185840
  names both proteins but reports mitochondrial/cytoplasmic localization and
  S. cerevisiae complementation only for Pmf1p PMID:12185840. Those experiments must not be presented as direct
  evidence for mmf2. Functional redundancy or division of labor between the paralogs,
  and which serine/threonine dehydratases generate mmf2's substrate, remain open.

Annotation-by-annotation reasoning (GOA)

Note: existing-annotation term ids are trusted (from GOA) — do not rewrite.

Core function summary (for core_functions)

mmf2 is, by family assignment and retention of the catalytic active-site arginine,
a RidA/Rid-family reactive enamine/imine deaminase (a "metabolite-damage
pre-emption" / hydrolase-type enzyme) that most plausibly hydrolyzes the reactive
enamine 2-aminoacrylate (and/or 2-iminopropanoate/2-iminobutanoate) to the stable
2-oxo acid, acting in the mitochondrial matrix. By analogy to the S. cerevisiae
ortholog Mmf1p and human UK114, its likely physiological role is protecting
mitochondrial PLP-dependent enzymes (and thereby indirectly mitochondrial genome
integrity) from enamine/imine damage arising from serine/threonine catabolism. The
specific in-vivo substrate and phenotype in pombe are not experimentally established.

The orthology/localization inference remains asymmetric: UniProt assigns mmf2 to
PANTHER PTHR11803:SF58 PROTEIN HMF1-RELATED, named after the cytosolic budding-yeast
paralog, whereas the matrix ISO and much of the physiological analogy use mitochondrial
Mmf1p. A subfamily name alone does not settle orthology, but the PAINT/PANTHER tree
placement must be reconciled before treating either branch as definitive.
[mmf2-uniprot.txt "DR PANTHER; PTHR11803:SF58; PROTEIN HMF1-RELATED; 1."]

An OpenScientist hypothesis review independently reached the same bounded conclusion:
GO:0120241 is supported for mmf2 as an inferred ISS/ISO annotation, not as IDA, and
the direct S. pombe Pmf1p experiments must not be transferred across the paralog
boundary. [file:SCHPO/mmf2/mmf2-hypotheses/core-function-schizosaccharomyces-pombe-mmf2-is-a-mitochondrial-rid-family-enzyme-whose-specific/openscientist.md
"The seed hypothesis is supported"]