SDD3 (systematic name YOL098C) is a ~1037-residue cytoplasmic protein of the peptidase M16 family (pitrilysin/inverzincin clan ME). It contains the two characteristic M16 domains (Pfam Peptidase_M16 N-terminal catalytic domain and Peptidase_M16_C C-terminal domain; MEROPS M16.A04) and retains the family's inverted zinc-binding catalytic motif HxxEH near its N-terminus, so it is predicted to be a zinc-dependent metalloendopeptidase; a genome-wide zinc-proteome survey computationally classified it as a zinc-binding protein. Despite the intact catalytic motif, no proteolytic activity, substrate, or cleavage specificity has been experimentally demonstrated for SDD3 or for any member of its uncharacterized ortholog group (PANTHER subfamily PTHR43016:SF16, with orthologs in fission yeast, worm and filamentous fungi), so it remains a putative metalloprotease. The protein localizes to the cytoplasm. The only reported phenotype comes from overexpression: multicopy expression of SDD3 suppresses the degenerative cell death caused by the dominant mitochondrial ADP/ATP carrier allele AAC2(A128P), placing it in a large cytosolic network that counteracts stress from over-accumulated, unimported mitochondrial precursor proteins. Its normal (loss-of-function) biological role and its physiological substrate remain undetermined.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Generic metal ion binding, inferred electronically from the InterPro M16 metalloenzyme signature (IPR011249). Consistent with the domain and with the more specific zinc ion binding annotation, but uninformative on its own. Reason: Domain-consistent (SDD3 carries the M16 inverted zincin fold) but this is the generic parent of the more specific GO:0008270 zinc ion binding term already present, and it is electronic. Retain as supporting, non-core; the specific zinc term better captures the predicted cofactor. |
| GO:0008270 zinc ion binding | RCA PMID:30358795 The cellular economy of the Saccharomyces cerevisiae zinc pr... | KEEP AS NON CORE | Summary: Zinc ion binding predicted by a proteome-wide zinc-proteome bioinformatic survey and independently consistent with the retained M16 HxxEH zincin motif (His60/Glu63/His64). Not a direct experimental binding measurement for SDD3. Reason: Defensible as a domain- and prediction-supported molecular-function hypothesis: the M16 fold uses a zinc cofactor and the catalytic motif is intact. However the evidence is computational (RCA zinc-proteome prediction) with no biochemical validation for SDD3 specifically, so it is kept as non-core. Zinc binding, if real, would be in service of the (still-undemonstrated) metalloendopeptidase activity rather than being the biological point of the gene. Supporting Evidence: PMID:30358795 identified using a bioinformatics analysis that combined global domain searches with local motif searches |
| GO:0005737 cytoplasm | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Cytoplasmic localization determined experimentally by genome-wide GFP-fusion microscopy, and independently consistent with the report that the anti-degenerative suppressor network (which includes SDD3) is cytosolic. Reason: Experimental (HDA) evidence from a canonical high-coverage yeast localization dataset; corroborated by the Wang & Chen 2015 statement that all suppressors are located in the cytosol. This is the single most solid annotation for SDD3 and represents its established subcellular location. The more precise term GO:0005829 (cytosol) is used in core_functions. Supporting Evidence: PMID:26192197 All of the suppressors are located in the cytosol, suggesting that they prevent cell death via pathways that operate in the cytosol |
| GO:0008150 biological_process | ND GO_REF:0000015 | KEEP AS NON CORE | Summary: Root biological_process term with ND (no data) evidence — a placeholder indicating that no biological process has been experimentally assigned to SDD3. Reason: This ND root annotation honestly reflects the current state of knowledge: the normal biological role of SDD3 is undetermined. The only reported phenotype is an overexpression suppression of AAC2(A128P) cell death, a gain-of-function genetic observation rather than a loss-of-function process assignment; inventing a specific BP term (e.g. proteostasis or protein catabolism) would over-annotate. Retain the ND placeholder rather than remove. Knowledge gap: The normal (loss-of-function) biological process in which SDD3 participates is unknown; no SDD3 deletion phenotype has been reported that would assign it to a specific pathway. OPEN BIOLOGY BP_DARK Resolve: Phenotype an sdd3 deletion (and sdd3 deletion combined with mPOS-inducing lesions such as yme1 deletion or AAC2(A128P)); test whether endogenous SDD3 is required for, or induced by, mPOS. "The remaining eight include the uncharacterized YEL057C, YMR074C, YOL098C and the truncated YPR022C that are named SDD1-4 (Suppressor of Degenerative Death) respectively" — PMID:26192197 |
| GO:0005829 cytosol | IC PMID:26192197 A cytosolic network suppressing mitochondria-mediated proteo... | NEW | Summary: More precise refinement of the experimental cytoplasm localization: SDD3 is a soluble cytosolic protein. Reason: Proposed as a more specific child of the accepted GO:0005737 (cytoplasm) experimental annotation. Supported by the genome-wide GFP localization (cytoplasm) and by the report that the anti-degenerative suppressor network including SDD3 is cytosolic. Supporting Evidence: PMID:26192197 All of the suppressors are located in the cytosol, suggesting that they prevent cell death via pathways that operate in the cytosol |
| GO:0004222 metalloendopeptidase activity | ISS PMID:30358795 The cellular economy of the Saccharomyces cerevisiae zinc pr... | NEW | Summary: Proposed domain-inferred molecular function: SDD3 is a peptidase M16 family protein retaining the canonical HxxEH zincin catalytic motif, so it is predicted to be a zinc-dependent metalloendopeptidase. Not experimentally demonstrated. Reason: Added as a hypothesis grounded in domain architecture (Pfam Peptidase_M16 + Peptidase_M16_C; MEROPS M16.A04; intact HxxEH motif at His60-Glu63-His64) and SGD's "putative metalloprotease" description, not as an asserted function. No catalytic activity or substrate has been measured for SDD3 or its SF16 subfamily; see the associated knowledge_gaps. Recorded so the predicted activity is explicit and testable rather than hidden. Supporting Evidence: PMID:30358795 identified using a bioinformatics analysis that combined global domain searches with local motif searches |
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Download this section (compressed HTML)Q: Is SDD3 a catalytically active zinc metalloendopeptidase, and what is its physiological substrate?
Suggested experts: Xin Jie Chen
Q: Does endogenous SDD3 have a loss-of-function role in cytosolic proteostasis or in clearing over-accumulated mitochondrial precursor proteins (mPOS), or is the suppression phenotype purely a high-copy gain-of-function effect?
Suggested experts: Xin Jie Chen
Experiment: Express and purify recombinant SDD3, assay metalloendopeptidase activity (zinc dependence, chelator sensitivity) against candidate M16-type peptide substrates, and compare wild-type with a catalytic HxxEH-motif mutant.
Hypothesis: SDD3 is a zinc-dependent metalloendopeptidase whose activity requires the intact HxxEH motif.
Type: in vitro enzyme assay with catalytic-residue mutagenesis
Experiment: Delete SDD3 and test for phenotypes in mPOS-sensitized backgrounds (e.g. yme1 deletion or AAC2(A128P)); use N-terminomics/degradomics and affinity-purification mass spectrometry in SDD3 over- vs under-expressing cells to identify substrates and interaction partners.
Hypothesis: SDD3 acts in cytosolic clearance of over-accumulated mitochondrial precursors.
Type: genetics plus interaction/degradomics proteomics
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: SDD3 has no experimentally demonstrated molecular function. Its assignment as a zinc metalloendopeptidase rests entirely on the presence of the M16 family fold and the intact HxxEH zincin motif plus a computational zinc-proteome prediction; no catalytic activity, substrate, cofactor binding, or physical interaction partner has been measured for the SDD3 protein.
OPEN BIOLOGY MF_DARK
What is known: Firmly known: SDD3 (YOL098C) is a verified, ~1037-aa, cytoplasmically localized (experimental GFP) protein of the peptidase M16 family that retains the canonical catalytic zincin motif, and whose multicopy overexpression suppresses AAC2(A128P)-induced degenerative cell death.
Significance: SDD3 is a conserved-but-dark member of the M16 peptidase family: its ortholog group (PANTHER subfamily PTHR43016:SF16 - fission yeast, worm, and filamentous fungi) is uniformly uncharacterized, so closing this gap would define function for a whole conserved subfamily rather than a single gene.
What would resolve it: Reconstitute and assay the predicted metalloendopeptidase activity in vitro (with catalytic-motif controls), identify substrates by degradomics, and map physical interactors by affinity-purification mass spectrometry.
Provenance (the field's own admissions):
Gap: It is unknown whether SDD3's recovery as an overexpression suppressor of mitochondria-mediated cell death reflects a genuine endogenous role in cytosolic proteostasis / clearance of over-accumulated mitochondrial precursors, or an indirect gain-of-function effect of high-copy expression.
OPEN BIOLOGY BP_DARK
What is known: SDD3 was identified only through multicopy overexpression suppression of AAC2(A128P)-induced death and belongs to a large cytosolic network the authors link to relief of mitochondrial Precursor Over-accumulation Stress (mPOS); the network as a whole acts by modulating cytosolic translation, mRNA turnover, and protein chaperoning/turnover, and all its members are cytosolic.
Significance: The distinction matters for whether SDD3 should ultimately be annotated to a proteostasis / protein-catabolism process and for understanding the crosstalk between mitochondrial dysfunction and cytosolic protein homeostasis relevant to neurodegeneration and ageing.
What would resolve it: Test the endogenous requirement (deletion and conditional depletion) in mPOS-sensitized backgrounds; measure whether SDD3 protein or transcript is induced under mPOS and whether it associates with, or degrades, accumulated mitochondrial precursor proteins.
Provenance (the field's own admissions):
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