Sdhaf2

UniProt ID: A0A494B8X4
Organism: Mus musculus
Review Status: COMPLETE
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Gene Description

Sdhaf2 (succinate dehydrogenase complex assembly factor 2; SDH5/Sdh5/SdhE family, PANTHER PTHR12469:SF2) is a nuclear-encoded mitochondrial matrix protein that binds the flavoprotein subunit SDHA of respiratory complex II and, acting as a dedicated chaperone-like assembly factor rather than an enzyme, promotes covalent attachment of FAD to SDHA and thereby assembly of active succinate dehydrogenase. The canonical mouse product is Q8C6I2 (164 aa). A0A494B8X4 is a 135-residue alternative product of the same gene (Ensembl ENSMUSP00000157391) that is identical to the canonical protein over residues 1-121, including the mitochondrial transit peptide, the N-terminal helical bundle and the glycine equivalent to human Gly78 that is needed for SDHA binding, but replaces canonical residues 122-164 with an unrelated 14-residue tail. It therefore lacks the C-terminal part of the Sdh5 domain (Pfam PF03937 66-141 in the canonical product, 66-124 here), including the helix corresponding to human residues 135-145 and the C-terminal helical segment. It is expected to be imported into mitochondria; whether it folds, binds SDHA or supports flavinylation has not been tested.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005759 mitochondrial matrix
IEA
GO_REF:0000044 		ACCEPT
Summary: Matrix localization is well grounded for the gene product. The eukaryotic PAINT node PTN000279729 of PTHR12469, which contains this mouse product through subfamily SF2, carries an IBD for mitochondrion (GO:0005739) seeded by yeast Sdh5, human SDHAF2 and Arabidopsis SDHAF2. SDHAF2 acts on SDHA, a matrix-facing protein, and A0A494B8X4 keeps the complete 27-residue mouse transit peptide, identical to the canonical Q8C6I2. The UniProt SubCell line behind this row is itself an ARBA prediction, so it is not quoted here. Mitochondrial matrix is as precise as the evidence allows and is the most confidently transferable property of this alternative product.
Reason: Accepted on the basis of the retained targeting peptide (re-review structural mapping) and the PAINT eukaryotic-node placement; no product-specific localization assay exists.
Supporting Evidence:
file:mouse/Sdhaf2/Sdhaf2-bioinformatics/RESULTS-rereview.md
| Mitochondrial transit peptide | 1-29 | Yes (mouse 1-27, identical to Q8C6I2) |
file:mouse/Sdhaf2/Sdhaf2-bioinformatics/RESULTS.md
| Transit peptide: Mitochondrion | 1–27 | 27 / 27 | 27 |
PMID:19628817
we investigated an uncharacterized but highly conserved mitochondrial protein (named here Sdh5)
GO:0010719 negative regulation of epithelial to mesenchymal transition
IEA
GO_REF:0000117 		MARK AS OVER ANNOTATED
Summary: ARBA association rule echoing a single lung-cancer study (PMID:23983127) in which loss of SDH5 was followed by EMT marker changes in cell lines, tumour specimens and SDH5 knockout mouse lung epithelium. That is a downstream cellular phenotype of losing a mitochondrial complex II assembly factor, not evidence that the protein performs a step in regulating EMT. PAINT curators placed mitochondrial, complex II assembly, TCA-cycle and succinate-to-ubiquinone electron-transport terms on the eukaryotic node PTN000279729 and did not propagate EMT or Wnt regulation, which is read as a deliberate decision. For this alternative product, which lacks the C-terminal part of the Sdh5 domain and was never assayed, the involved_in claim is an over-annotation.
Reason: Knockout/knockdown phenotype (necessity) does not establish participation; electronic ARBA transfer to a truncated alternative product with no phylogenetic support for the term. The experimentally based gene-level association, if any, belongs on the canonical product with an acts_upstream_of_or_within qualifier.
Supporting Evidence:
PMID:23983127
In SDH5 knock-out mice, lung epithelial cells exhibited elevated mesenchymal markers, which is characteristic of EMT.
file:mouse/Sdhaf2/Sdhaf2-bioinformatics/RESULTS-rereview.md
| Helix 135-145 | | No: aligned positions are the unrelated tail (2/11 identical) |
GO:0090090 negative regulation of canonical Wnt signaling pathway
IEA
GO_REF:0000117 		MARK AS OVER ANNOTATED
Summary: ARBA association rule derived from the same lung-cancer study (PMID:23983127), which reported that SDH5 modulates GSK-3-beta/beta-catenin signalling in human lung-cancer cells. The claim rests on one cell-context study and has not been placed by PAINT on any PTHR12469 node, whereas the conserved, structurally characterised role of the family is SDHA flavinylation inside mitochondria. A cytosolic Wnt-regulatory activity for a matrix-targeted assembly factor is not established, and nothing is known about it for the C-terminally altered A0A494B8X4 product. Over-annotation for this product.
Reason: Single context-dependent study, no phylogenetic support (absent from PAINT IBD set), and the target is an unassayed alternative product lacking part of the Sdh5 domain.
Supporting Evidence:
PMID:23983127
SDH5 functions as a negative regulator of Wnt-Ξ²-catenin signaling.

Core Functions

Gene-level function of Sdhaf2, inherited from the PTHR12469 eukaryotic node PTN000279729: a mitochondrial matrix assembly factor that binds SDHA and licenses covalent FAD attachment for complex II assembly. For the A0A494B8X4 alternative product only mitochondrial (matrix) targeting is confidently retained; the molecular activity is not asserted here because the product lacks the C-terminal part of the Sdh5 domain and has not been assayed.

Cellular Locations:
mitochondrial matrix
Supporting Evidence:
  • PMID:19628817
    Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination
  • PMID:32887801
    works in synergy with SDHAF2 to properly orient the flavin and
  • file:mouse/Sdhaf2/Sdhaf2-bioinformatics/RESULTS-rereview.md
    The product keeps the targeting peptide, the N-terminal helical bundle and the RGxxE

References

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Suggested Questions for Experts

Q: Does the 135-residue mouse product bind SDHA and promote covalent FAD attachment after mitochondrial import?

Q: Is the GSK-3-beta/beta-catenin effect of SDH5 loss (PMID:23983127) a direct activity of SDHAF2 or a secondary consequence of complex II deficiency (e.g. succinate accumulation)?

Suggested Experiments

Experiment: Express A0A494B8X4 and the canonical Q8C6I2 in Sdhaf2-null mouse cells and compare mitochondrial import, co-immunoprecipitation with SDHA, covalent flavin content of SDHA (in-gel flavin fluorescence) and complex II activity.

External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

ProtNLM2 External predictions

View prediction review YAML Β· Sdhaf2-protnlm-predictions-review.yaml Β· Review status: COMPLETE

ProtNLM2 (UniProt API snapshot 2026-09-10) emitted three GO terms for A0A494B8X4, a 135-residue alternative product of mouse Sdhaf2 that is identical to the canonical Q8C6I2 over residues 1-121 but replaces the C-terminal part of the Sdh5 domain with an unrelated 14-residue tail. Mitochondrial matrix is correct and already annotated to this product (CNN), supported by the retained transit peptide and the conserved mitochondrial location of Sdh5/SDHAF2. Protein-FAD linkage is the established gene-level role of SDHAF2 and is carried by the canonical product, but whether this truncated product binds SDHA and supports flavinylation is untested (UNC). Succinate-to-ubiquinone electron transport is carried out by assembled complex II; Sdhaf2 is an assembly factor upstream of it, and the gene review marks the same term an over-annotation on the canonical product (NPI).

Source documents: genes/mouse/Sdhaf2/Sdhaf2-protnlm-source.json Β· genes/mouse/Sdhaf2/Sdhaf2-ai-review.yaml Β· genes/mouse/Sdhaf2__Q8C6I2/Sdhaf2__Q8C6I2-ai-review.yaml Β· genes/mouse/Sdhaf2/Sdhaf2-bioinformatics/RESULTS-rereview.md

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0018293 protein-FAD linkage GO_BP
UNC β€” Uncertain Review score: 1/2
Prediction method: ProtNLM2 Β· Version: UniProt API snapshot 2026-09-10 Β· file:mouse/Sdhaf2/Sdhaf2-protnlm-source.json
Review rationale: Protein-FAD linkage is the conserved role of the Sdh5/SDHAF2 family, shown experimentally for yeast and human orthologs, and the gene already carries this term on the canonical product Q8C6I2 (ISO/ISS, accepted in that review), so it would not be novel at the gene level. For A0A494B8X4 itself the claim is unresolved: the product keeps the transit peptide, the N-terminal helical bundle and the Gly78-equivalent residue, but lacks the C-terminal helices of the Sdh5 domain, and it has never been tested for folding, SDHA binding or flavinylation. The gene review for this product deliberately withholds the activity for the same reason. Without product-specific evidence the prediction can be neither confirmed nor refuted.
Supporting Evidence:
GO:0005759 mitochondrial matrix GO_CC
CNN β€” Correct but not novel Review score: 2/2
Prediction method: ProtNLM2 Β· Version: UniProt API snapshot 2026-09-10 Β· file:mouse/Sdhaf2/Sdhaf2-protnlm-source.json
Review rationale: A0A494B8X4 already carries mitochondrial matrix in GOA (GO_REF:0000044), and the gene review accepts it; the canonical product carries the same term. The location is supported independently of that electronic row: the product retains the complete 27-residue mouse transit peptide identical to Q8C6I2, and Sdh5/SDHAF2 orthologs are conserved mitochondrial proteins acting on the matrix-facing SDHA subunit. The prediction is correct but not novel.
Supporting Evidence:
GO:0006121 mitochondrial electron transport, succinate to ubiquinone GO_BP
NPI β€” Nonparalog incorrect Review score: 0/2
Prediction method: ProtNLM2 Β· Version: UniProt API snapshot 2026-09-10 Β· file:mouse/Sdhaf2/Sdhaf2-protnlm-source.json
CURATION MISTAKE
Review rationale: Electron transfer from succinate to ubiquinone is performed by assembled complex II (SDHA-SDHD). Sdhaf2 is an assembly factor that binds SDHA and promotes its covalent flavinylation before complex assembly; it does not transfer electrons and is not part of the mature complex. Loss of Sdh5 abolishes SDH-dependent respiration, which shows necessity, not participation. The canonical-product review marks every GOA row for this term (IBA, UniRule IEA, ISO) as an over-annotation on these grounds, so the prediction most likely reproduces that over-propagated annotation. The appropriate process terms for the gene are complex II assembly and protein-FAD linkage, and for this truncated, unassayed product even those are unconfirmed.
Supporting Evidence:
  • PMID:19628817: "Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination"
  • PMID:38569044: "Restoration of Sdhaf2 normalized complex II activity, lipid oxidation, and insulin action in Drp1-KD myocytes."

Deep Research

Falcon

(Sdhaf2-deep-research-falcon.md)

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πŸ“š Additional Documentation

Notes

(Sdhaf2-notes.md)

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Bioinformatics Results

(RESULTS.md)

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Protnlm Function Review

(Sdhaf2-protnlm-function-review.md)

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πŸ“„ View Raw YAML

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