VAPA (vesicle-associated membrane protein-associated protein A) is a tail-anchored protein of the endoplasmic reticulum membrane. A C-terminal transmembrane helix holds it in the ER while its N-terminal major sperm protein (MSP) domain faces the cytosol and binds FFAT and phospho-FFAT motifs in partner proteins such as oxysterol-binding protein-related proteins, STARD3 and other lipid-transfer and trafficking factors. Acting as a docking platform, VAPA recruits these partners to the ER surface and helps form membrane contact sites between the ER and endosomes, Golgi and the plasma membrane; the lipid transfer itself is carried out by the recruited partners. A minor pool has been reported at the plasma membrane and at epithelial tight junctions. This horse entry encodes the longer VAPA splice form, which carries an extra segment of about 45 residues in the linker between the MSP domain and the coiled-coil region, equivalent to human VAPA isoform 2; the MSP domain, coiled coil and membrane anchor are intact.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000120 | ACCEPT | Summary: ER membrane residence through the C-terminal tail anchor is the defining location of VAPA and is conserved in the horse protein. Reason: The horse protein belongs to PANTHER subfamily PTHR10809:SF155 (VAPA), the same subfamily as human VAPA (Q9P0L0), and PAINT curators placed ER membrane at the deep VAP node PTN000087323, from which human VAPA receives its IBA; the horse protein descends from that node. It aligns gaplessly to human VAPA isoform 2 over all 294 residues at 95.9% identity, with the Phobius-predicted C-terminal helix (273-293) in the position of the human type IV anchor. Structural and cell-biology work on human VAPA establishes the ER-anchored topology with the MSP domain in the cytosol. ARBA localization text in the horse entry is not used as support. Supporting Evidence: PMID:33124732 VAP‐A, VAP‐B, and MOSPD2 are anchored in the ER membrane by a carboxyl‐terminal transmembrane domain with their MSP domain projecting into the cytosol. file:HORSE/VAPA/VAPA-uniprot.txt TRANSMEM 273..293 file:HORSE/VAPA/VAPA-bioinformatics/RESULTS-rereview.md | Q9P0L0-2 (VSP_038648) | 294 | 294 | 294 | 282 | 95.9% | 0 / 0 | |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: A plasma-membrane pool of VAPA is reported for mammalian VAPA and was propagated by PAINT across the VAP family; it is peripheral to the ER-anchored adaptor role. Reason: Human VAPA was detected at the plasma membrane with occludin in polarized epithelia, and PAINT propagated plasma membrane from the same deep node (PTN000087323) that carries ER membrane, so the location is a phylogenetically considered inference that covers this SF155 member. The bulk of VAPA is in the ER and its core adaptor activity is exercised from the ER side of contact sites, so this location is kept as non-core. No horse imaging data exist. Supporting Evidence: PMID:10523508 Antibodies to the human VAP-33 co-localized with occludin at the tight junction in many tissues and tissue culture cell lines. |
| GO:0005923 bicellular tight junction | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: Tight-junction localization rests on one 1999 antibody colocalization study of human VAPA and was not propagated by PAINT; the electronic transfer to horse overstates the evidence. Reason: The only experimental basis is antibody colocalization of human VAP-33/VAPA with occludin (PMID:10523508, abstract only). PAINT curators propagated ER membrane and plasma membrane from the VAP node PTN000087323 but did not propagate bicellular tight junction, although the human IDA was available to them; per campaign rules this omission is treated as a deliberate judgment. The horse row comes from a UniProt subcellular-location mapping of ARBA-predicted text rather than from phylogenetic inference, and the later literature on VAPA localizes it to the ER and to ER-organelle contact sites rather than to junctional complexes. The term is not demonstrably wrong, so it is flagged as an over-annotation rather than removed. Supporting Evidence: PMID:10523508 Antibodies to the human VAP-33 co-localized with occludin at the tight junction in many tissues and tissue culture cell lines. |
| GO:0043495 protein-membrane adaptor activity | IBA GO_REF:0000033 | NEW | Summary: Proposed new annotation. VAPA recruits FFAT-bearing cytosolic proteins to the ER membrane, and PAINT placed this activity at the VAP node from which the horse SF155 member descends. Reason: The horse entry has no molecular-function annotation. Human VAPA carries protein-membrane adaptor activity by IDA in several studies and by IBA from PAINT node PTN000087323; the horse protein is in the same PANTHER subfamily (PTHR10809:SF155), so it inherits from that node. The residues that form the FFAT-binding pocket of human VAPA (K50, K52, T53, T54, K94, F95, M96, K125) are all identical in the horse protein, and the C-terminal membrane anchor is retained, so both halves of the adaptor (partner binding and membrane anchoring) are present. The extra linker segment shared with human isoform 2 lies outside the MSP domain and the anchor. This proposal is evidenced by phylogenetic placement plus residue conservation; it is not a horse experiment. FFAT motif binding (GO:0033149) is not proposed separately because PAINT did not propagate it, and the adaptor term already captures the role. Supporting Evidence: PMID:33124732 F207, the second residue of the FFAT motif, was bound to the hydrophobic pocket at the surface of the MSP domain constituted by aliphatic parts of the side chains of K52, T54, K94, M96, and K125 of VAP‐A file:HORSE/VAPA/VAPA-bioinformatics/RESULTS-rereview.md | 94 | K | 94 | K | True | file:HORSE/VAPA/VAPA-bioinformatics/RESULTS-rereview.md | 96 | M | 96 | M | True | |
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Download this section (compressed HTML)Q: Does the linker insertion that distinguishes VAPA isoform 2 (present in this horse gene model) alter partner selection, dimerization or contact-site formation compared with the shorter isoform?
Experiment: Express the long (isoform 2-like) and short horse VAPA forms in VAPA/VAPB double-knockout cells and compare recruitment of FFAT partners (OSBP, STARD3) and ER-endosome contact formation.
Type: complementation and imaging
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