LITAFD is a 72-residue protein that consists of a single LITAF (SIMPLE-like) domain, the conserved C-terminal domain of the CDIP1/LITAF family. It shares about 47% identity with the LITAF domain of LITAF and about 37% with that of CDIP1, but has none of the proline-rich N-terminal sequence of either. Both cysteine-rich zinc-knuckle motifs (CPYC and CPVC) and the intervening hydrophobic amphipathic segment are conserved. In LITAF and CDIP1 this arrangement forms a zinc-stabilised domain that inserts monotopically into the cytoplasmic leaflet of endosomal and lysosomal membranes. LITAFD is therefore expected to be a zinc-binding peripheral membrane protein. The gene is conserved across vertebrates and is expressed predominantly in testis. Protein existence is inferred from homology only, and nothing is known about its localisation, binding partners or biological role.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001817 regulation of cytokine production | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Inherited from mouse Litaf (the only donor) through PANTHER node PTN000591246. LITAFD itself has never been tested, it is expressed mainly in testis, and it lacks the LITAF N-terminal region. Reason: The donor evidence concerns LITAF in LPS-stimulated macrophages, where LITAF was first described as a TNF-alpha transcription regulator. That context does not obviously carry over to a testis-enriched paralog that is only the membrane-binding LITAF domain. The family members that have been characterised biochemically (LITAF, CDIP1) act through membrane insertion at endosomes. Cytokine regulation by LITAF is a cell-type-specific downstream outcome, not an intrinsic property of the domain. LITAFD is a real, conserved gene, so the product probably exists. The term is not shown to be wrong, but nothing supports it beyond inheritance from one mouse gene. Propagation Review Root cause: PROPAGATION BAD Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: PANTHER:PTN000591246 · PTN000591246 SUPPORTS SOURCE BUT NOT TARGET The node is seeded only by mouse Litaf, from macrophage/LPS biology. Placing it above the testis-enriched LITAFD subfamily (PTHR23292:SF27) extends a cell-type-specific outcome to a paralog that has the domain alone. Supporting Evidence: file:human/LITAFD/LITAFD-bioinformatics/RESULTS.md LITAFD consists of the LITAF domain and nothing else. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Nuclear localisation inherited from LITAF and CDIP1. LITAFD is a membrane-insertion domain with no other sequence, and there is no evidence for a nuclear pool. Reason: LITAF and CDIP1 carry nuclear annotations, linked to the proposed transcription-factor role of LITAF and to CDIP1 as a p53 target. However, both proteins integrate monotopically into endosomal membranes through the LITAF domain, which faces the cytoplasm. LITAFD has nothing beyond that domain and no nuclear targeting sequence, and its localisation has not been studied. The same node (PTN008386299) correctly carries the endosomal and lysosomal membrane terms. The nuclear term is the weakest of the three for a domain-only paralog, so it is flagged rather than removed. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN008386299 · PTN008386299 SUPPORTS SOURCE BUT NOT TARGET LITAF and CDIP1 have nuclear observations, but those are not a property of the LITAF domain, which is all that LITAFD has. The endosomal/lysosomal terms from the same node transfer more safely. Supporting Evidence: PMID:27582497 The related human protein, CDIP1 (cell death involved p53 target 1), displays identical membrane topology, suggesting that this mode of membrane integration is conserved in LITAF family proteins. file:human/LITAFD/LITAFD-bioinformatics/RESULTS.md LITAFD lacks every sequence outside the domain |
| GO:0008270 zinc ion binding | IBA GO_REF:0000033 | ACCEPT | Summary: Sound inheritance. All four zinc-ligand cysteines of LITAF, in two CXXC knuckles, are conserved in LITAFD (C7, C10, C59, C62), and LITAF binds one zinc per molecule. Reason: Zinc binding is an intrinsic property of the LITAF domain. LITAF has direct evidence (1 mol/mol zinc, and mutating the ligands disrupts membrane association). LITAFD sits inside the family, and every ligand position is retained. This is the clearest molecular property that can be assigned to LITAFD, although it has not been measured on the LITAFD protein itself. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000591207 · PTN000591207 SUPPORTS TRANSFER LITAF IDA (PMID:27582497) seeds a domain-intrinsic property; the target retains all four Cys ligands. Supporting Evidence: PMID:27582497 Recombinant LITAF contains 1 mol/mol zinc, while mutation of predicted zinc-binding residues disrupts LITAF membrane association. file:human/LITAFD/LITAFD-bioinformatics/RESULTS.md All four annotated Zn(2+) ligands of LITAF (C96, C99, C148, C151) and of CDIP1 |
| GO:0016020 membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Supported. The amphipathic membrane-insertion segment of the LITAF domain is conserved in LITAFD (residues 22-45, aligned without gaps to LITAF 111-134). Reason: The UniProt SubCell keyword (peripheral membrane protein) rests on the PROSITE LITAF rule. Membrane association is the defining biochemical behaviour of the domain, shown for both LITAF and CDIP1. The broad term is appropriate while the specific compartment of LITAFD remains unknown. Supporting Evidence: PMID:27582497 we conclude that LITAF is a monotopic membrane protein whose membrane integration is stabilised by a zinc finger file:human/LITAFD/LITAFD-bioinformatics/RESULTS.md The LITAF membrane-binding amphipathic helix (residues 111-134, |
| GO:0098560 cytoplasmic side of late endosome membrane | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: A defensible inheritance of the family's monotopic endosomal topology, which the LITAF domain supplies. It has not been tested for LITAFD. Reason: CDIP1 and LITAF localise to late endosomes and lysosomes with the LITAF domain on the cytoplasmic face. LITAFD keeps the zinc knuckles and the hydrophobic segment that drive this insertion, so the transfer is plausible. However, its subcellular localisation has never been examined, and the N-terminal regions of LITAF and CDIP1 that LITAFD lacks may contribute to compartment selection. The specific organelle is therefore kept as non-core rather than accepted. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN008386299 · PTN008386299 SUPPORTS TRANSFER Seeded by CDIP1 IDA and LITAF localisation data; the domain responsible for the topology is retained in the target, but compartment specificity untested. Supporting Evidence: PMID:27582497 epitope-tagged CDIP1 localised predominantly to CD63-positive late endosomes as well as to LAMP1-positive compartments |
| GO:0098574 cytoplasmic side of lysosomal membrane | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: As for the late endosome term: plausible inheritance of the LITAF-domain topology, not tested for LITAFD. Reason: LITAF localises extensively, and CDIP1 partly, to LAMP1-positive late endosomes/lysosomes with the domain facing the cytoplasm. LITAFD conserves the membrane-insertion machinery, but its own compartment is unknown. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN008386299 · PTN008386299 SUPPORTS TRANSFER Same node and donors as the late-endosome term; domain-intrinsic topology retained, compartment untested in the target. Supporting Evidence: PMID:27582497 Endogenous LITAF localised partially to EEA1-positive early endosomes and more extensively to LAMP1-positive late endosomes/lysosomes (Figure 2A). |
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Download this section (compressed HTML)Q: Is LITAFD protein detectable in testis (for example in spermatogenic cells), and does it localise to late endosomes/lysosomes like LITAF and CDIP1, or to a germ-cell compartment such as the acrosome?
Q: Should the PANTHER nodes carrying LITAF-specific biology (nucleus at PTN008386299, regulation of cytokine production at PTN000591246) be narrowed so that they do not cover the domain-only LITAFD subfamily (PTHR23292:SF27)?
Experiment: Express tagged LITAFD in cultured cells and in testis tissue sections, and co-stain with markers for early endosomes, late endosomes and lysosomes, alongside zinc-ligand (C7/C10/C59/C62) mutants. This would test whether membrane association depends on zinc as it does for LITAF.
Experiment: Use targeted proteomics or an antibody to confirm the endogenous protein in human testis, raising protein existence above homology inference.
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