AKAP10, also called dual-specific A-kinase anchoring protein 2 (D-AKAP2), is a 662-residue scaffold protein with no catalytic domain, no nucleotide- or metal-binding site and no EC number. Its chain is built from three interaction modules separated by disordered linkers: two tandem regulator-of-G-protein-signalling (RGS) domains in the N-terminal half (residues 125-369 and 379-505), an amphipathic A-kinase-binding helix near the C-terminus (residues 629-653), and a class-I PDZ-binding motif at the extreme C-terminus. Its defining activity is anchoring cAMP-dependent protein kinase. The C-terminal helix docks into the dimerization/docking domain of the protein kinase A regulatory subunit, and it does so for both type I and type II regulatory subunits, which is what makes it dual-specific; the two complexes differ in the register with which the same helix packs against the R-subunit dimer. Only the regulatory subunit has ever been assayed, never the catalytic one. Immediately downstream of that helix, the PDZ-binding motif engages PDZ-domain scaffolds, PDZK1 most strongly, and the two motifs become ordered only on binding, so a single short segment presents an alpha-helix to the kinase and a beta-strand to the PDZ domain. Because formation of the kinase complex precedes high-affinity PDZ engagement, AKAP10 nucleates a polyvalent assembly that reaches membrane transporters indirectly, through the PDZ scaffold, rather than by contacting a membrane protein itself. The tandem RGS domains do not act as GTPase activators on heterotrimeric G-protein alpha subunits: the Galpha transition-state contact residues of a canonical RGS box are absent from both domains, and no activation of a heterotrimeric G protein has ever been measured. What the two domains do, acting as a single functional unit, is bind the small GTPases Rab4 and Rab11 - Rab4 preferentially in its GTP-bound state. Through this surface AKAP10 associates with Rab4/Rab11-positive recycling endosomes and retains cargo there: depleting it redistributes Rab11 and the transferrin receptor toward the cell periphery and accelerates transferrin recycling, so the protein normally slows traffic out of the endocytic recycling compartment. Where the protein sits is genuinely contested. Endogenous AKAP10 is reported as highly enriched in mitochondria in human, mouse and rat tissue, and it appears in high-confidence human mitochondrial proteomes; a later study in HeLa cells found the endogenous protein almost entirely cytosolic with very little mitochondrial colocalisation, and attributed the discrepancy to antibody cross-reactivity or cell type. The N-terminal mitochondrial transit peptide that gives the protein its name is a sequence-based prediction, and the entry contains no transmembrane segment and no lipid-binding domain, so the mechanism of membrane attachment is unresolved. A common coding variant, Ile646Val in the A-kinase-binding helix, is carried by roughly 40 percent of human alleles and is associated in population data with a higher basal heart rate and reduced heart-rate variability; the molecular basis of that association is not known.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:20159461 Structure of D-AKAP2:PKA RI complex: insights into AKAP spec... | MODIFY | Summary: The AKAP10:PKA-RI crystal structure, recorded as bare protein binding. The partner is the PKA type I-alpha regulatory subunit and the interaction is solved at 2.28 A, so an informative term is available and should be used. Reason: P00514 resolves to KAP0_BOVIN, reviewed Swiss-Prot, 380 aa - the canonical bovine PKA RI-alpha entry, which UniProt's own INTERACTION block flags as Xeno. The AKAP10 side of the experiment is human: UniProt cross-references the structure as "DR PDB; 3IM4; X-ray; 2.28 A; C=623-662.", i.e. chain C is human AKAP10 residues 623-662, and the resulting helix is recorded in the feature table as "FT HELIX 629..653". IntAct lists this partner under two methods, x-ray diffraction and fluorescence spectroscopy, so it is not a single-modality claim. GO:0005515 conveys nothing here. Every AKAP10 experiment, in this paper and in PMID:25097019 and PMID:25348485, assays binding to the regulatory subunit dimerization/docking domain; none assays the catalytic subunit. GO:0034237 protein kinase A regulatory subunit binding is an active is_a child of GO:0051018 (verified via QuickGO: isObsolete false, no secondaryIds, no children) and states exactly what was measured. The has_input extension records the human orthologue of the assayed partner; the bovine accession stays in supporting_entities because that is the protein that was actually in the crystal. Proposed replacements: protein kinase A regulatory subunit binding Supporting Evidence: PMID:20159461 Here we have determined the structures of the RIalpha D/D domain alone and in complex with D-AKAP2. PMID:20159461 An unexpected shift in the helical register of D-AKAP2 compared to the RIIalpha:D-AKAP2 complex structure makes the mode of binding to RIalpha novel. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: GRID2IP (Delphilin), one of 21 PDZ-domain proteins whose affinity for the AKAP10 C-terminal PDZ-binding motif was measured in a proteome-scale holdup survey. What was measured is PDZ-domain binding, and GO can say so. Reason: A4D2P6 resolves to GRD2I_HUMAN, reviewed Swiss-Prot, 1211 aa - canonical, not an ORFeome fragment. All 25 accessions cited across this gene's GOA WITH/FROM column resolve to reviewed Swiss-Prot entries of canonical length (checked with entryType.startswith("UniProtKB reviewed"), since "reviewed" is a substring of "unreviewed"); none is a partial clone. The assay is a purified PDZ domain against the AKAP10 PDZ-binding motif, so the AKAP10-side activity is GO:0030165 PDZ domain binding (verified active, no children), which is both more informative than GO:0005515 and a more accurate description of the experiment than a claim about a cellular AKAP10-GRID2IP complex. IntAct lists this partner under holdup assay only, with no orthogonal method, so the partner identity is an in vitro affinity rather than a demonstrated cellular interaction; the term change captures the measured activity without asserting the complex. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: MPDZ (MUPP1), a 13-PDZ-domain scaffold, from the same holdup survey. Same reasoning as the other 20 rows from this reference. Reason: O75970 resolves to MPDZ_HUMAN, reviewed Swiss-Prot, 2070 aa - canonical. Holdup assay only in IntAct, no orthogonal method, no independent AKAP10 literature. The measured activity is binding of the AKAP10 PDZ-binding motif to a PDZ domain, so GO:0030165 is the right term; the cellular relevance of this particular pairing is untested. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: DLG4 (PSD-95), from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: P78352 resolves to DLG4_HUMAN, reviewed Swiss-Prot, 724 aa - canonical. Holdup assay only, three replicate rows in IntAct that are replicates of one assay rather than three experiments. GO:0030165 states the measured activity; no cellular AKAP10-DLG4 complex has been shown, and AKAP10 has no reported synaptic biology, so the partner identity is held as an in vitro affinity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: APBA1 (Mint1), from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q02410 resolves to APBA1_HUMAN, reviewed Swiss-Prot, 837 aa - canonical. Holdup assay only. GO:0030165 records the PDZ-domain binding that was measured; the cellular interaction is untested. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: TJP1 (ZO-1), from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q07157 resolves to ZO1_HUMAN, reviewed Swiss-Prot, 1748 aa - canonical. Holdup assay only. GO:0030165 records the measured activity without asserting a tight-junction role for AKAP10, for which there is no other evidence. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: DLG1 (SAP97), from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q12959 resolves to DLG1_HUMAN, reviewed Swiss-Prot, 904 aa - canonical. Holdup assay only. GO:0030165 records the measured activity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: Pro-interleukin-16, whose C-terminal PDZ domain was in the holdup panel. Same reasoning as the other 20 rows from this reference. Reason: Q14005 resolves to IL16_HUMAN, reviewed Swiss-Prot, 1332 aa - canonical. Holdup assay only. The measured event is PDZ-domain binding by the AKAP10 motif, and nothing about cytokine biology follows from it, which is precisely why GO:0030165 is the safe and informative term here. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: SCRIB, from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q14160 resolves to SCRIB_HUMAN, reviewed Swiss-Prot, 1655 aa - canonical. Holdup assay only. GO:0030165 records the measured activity; no polarity role for AKAP10 follows. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: NHERF2 (SLC9A3R2) measured by holdup. This is the one PDZ partner that a second, orthogonal method also reports (see the PMID:40205054 row), so it is the best-supported partner in this set after PDZK1. Reason: Q15599 resolves to NHRF2_HUMAN, reviewed Swiss-Prot, 337 aa - canonical. IntAct lists it under two different methods, holdup assay and anti tag coip, from two different publications, which no other member of the holdup panel achieves. GO:0030165 is the mechanism, and the AKAP10 C-terminal motif is the surface involved. A naming caution recorded here rather than silently resolved: the 2003 paper that first linked AKAP10 to NHERF scaffolds tested NHERF-1 (SLC9A3R1, O14745), which is not in GOA at all; the annotated partner Q15599 is NHERF2 (SLC9A3R2). They are different proteins and are not treated as interchangeable here. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: PDZK1 (NHERF3) measured by holdup - and, unlike the rest of the panel, a partner with independent pull-down, cellular recruitment and crystallographic support. This is the biologically real PDZ interaction. Reason: Q5T2W1 resolves to NHRF3_HUMAN, reviewed Swiss-Prot, 519 aa - canonical PDZK1. IntAct shows holdup only, which understates the case: PDZK1 binds AKAP10 in pull-downs and co-immunoprecipitates from transfected kidney cells (PMID:14531807), is recruited onto Rab11 endosomes by AKAP10 in HeLa cells and is not recruited by the construct lacking the terminal three residues (PMID:19797056), and appears in a ternary crystal structure with AKAP10 and PKA-RII in which AKAP10 presents a beta-strand to the PDZ domain (PMID:25348485). GO:0030165 PDZ domain binding is therefore not a hedge on this row but the mapped mechanism, and it is core: this is the second arm of the polyvalent scaffold, the arm that reaches membrane transporters. Note that AKAP10 reaches them indirectly - PMID:25348485 states that D-AKAP2 does not contact the membrane protein itself. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:14531807 In pull-down experiments, D-AKAP2 tightly bound PDZK1 as well as N+/H+ exchanger regulator factor (NHERF-1), but the latter with an apparent fourfold lower affinity. PMID:25348485 Formation of the D-AKAP2: PKA binary complex is an important first step for high affinity interaction with PDZK1, and the structure reveals important clues toward understanding this phenomenon. PMID:25348485 In contrast to many other AKAPs, D-AKAP2 does not interact directly with the membrane protein. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: FRMPD2, from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q68DX3 resolves to FRPD2_HUMAN, reviewed Swiss-Prot, 1309 aa - canonical. Holdup assay only. GO:0030165 records the measured activity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: MAGI2, from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q86UL8 resolves to MAGI2_HUMAN, reviewed Swiss-Prot, 1455 aa - canonical. Holdup assay only; the five IntAct rows are replicate holdup measurements, not five experiments. GO:0030165 records the measured activity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: NHERF4 (PDZD3), from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q86UT5 resolves to NHRF4_HUMAN, reviewed Swiss-Prot, 571 aa - canonical. Holdup assay only. Being a NHERF-family member makes this pairing plausible by analogy with PDZK1, but plausibility is not evidence, and no AKAP10-NHERF4 cellular experiment exists. GO:0030165 records what was measured. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: LNX2, from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q8N448 resolves to LNX2_HUMAN, reviewed Swiss-Prot, 690 aa - canonical. Holdup assay only. GO:0030165 records the measured activity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: PATJ (INADL), from the holdup survey. Its UniProt NbExp of 9 is the clearest case in this gene of replicate sub-measurements being read as independent experiments. Reason: Q8NI35 resolves to INADL_HUMAN, reviewed Swiss-Prot, 1801 aa - canonical. All nine IntAct rows are holdup assay; there is no second method and no second publication. The nine reflect the number of PATJ PDZ domains profiled against the AKAP10 motif, not nine independent demonstrations of a cellular complex. GO:0030165 records the measured activity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: LNX1, from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q8TBB1 resolves to LNX1_HUMAN, reviewed Swiss-Prot, 728 aa - canonical. Holdup assay only. GO:0030165 records the measured activity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: DLG3 (SAP102), from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q92796 resolves to DLG3_HUMAN, reviewed Swiss-Prot, 817 aa - canonical. Holdup assay only. GO:0030165 records the measured activity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: MAGI1, from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q96QZ7 resolves to MAGI1_HUMAN, reviewed Swiss-Prot, 1491 aa - canonical. Holdup assay only. GO:0030165 records the measured activity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: APBA2 (Mint2), from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q99767 resolves to APBA2_HUMAN, reviewed Swiss-Prot, 749 aa - canonical. Holdup assay only. GO:0030165 records the measured activity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: GRIP2, from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q9C0E4 resolves to GRIP2_HUMAN, reviewed Swiss-Prot, 1043 aa - canonical. Holdup assay only. GO:0030165 records the measured activity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MODIFY | Summary: GRIP1, from the holdup survey. Same reasoning as the other 20 rows from this reference. Reason: Q9Y3R0 resolves to GRIP1_HUMAN, reviewed Swiss-Prot, 1128 aa - canonical. Holdup assay only. GO:0030165 records the measured activity. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | MODIFY | Summary: NHERF2 again, this time from a multimodal cell-map study by affinity purification-mass spectrometry. Together with the holdup row it makes NHERF2 the only PDZ partner shown by two independent methods. Reason: IntAct records this as anti tag coip, a different method and a different publication from the holdup measurement of the same pair, so the two rows are genuinely independent rather than one experiment counted twice. The co-complex is cellular; the mechanism is supplied by the companion holdup measurement, which shows the AKAP10 PDZ-binding motif engaging a NHERF2 PDZ domain directly. GO:0030165 is therefore the informative term for the AKAP10 side of both rows. This reference is a systematic study contributing 3026 annotations across GOA, so the row is a cell of a proteome-scale matrix rather than a gene-directed finding; that is why it is the corroboration of the holdup result rather than the primary evidence. Proposed replacements: PDZ domain binding Supporting Evidence: PMID:36115835 Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Automatic cytoplasm call from an ARBA rule and the UniProt subcellular-location vocabulary. Correct but strictly the parent of GO:0005829, which this gene holds by its own human IDA. Reason: UniProt's own subcellular location line lists Cytoplasm with ECO:0000269|PubMed:11248059, so the underlying statement is experimentally sourced rather than invented by the rule. It is kept, but as the less informative ancestor of a term that already has direct human evidence on this gene, it adds nothing a curator would act on. Propagation Review Root cause: EVIDENCE CIRCULAR OR REDUNDANT Failure modes: GRANULARITY MISMATCH Sources checked: ARBA:ARBA00026971 · UniProt ARBA automatic rule - not a protein NOT RELEVANT A rule identifier, not a gene product, so it carries no evidence of its own. UniProtKB-SubCell:SL-0086 · UniProt controlled-vocabulary subcellular location Cytoplasm SUPPORTS TRANSFER Traces to the CC SUBCELLULAR LOCATION line, whose Cytoplasm term carries ECO:0000269|PubMed:11248059. |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: AKAP10 is a member of MitoCoP, the high-confidence human mitochondrial proteome built from four human cell lines by subtractive, spatial and import proteomics. This is the strongest human evidence for the mitochondrial location and, importantly, it does not depend on the antibody that a later study questioned. Reason: The mitochondrial localisation of this protein is contested in the primary literature: endogenous protein was reported highly enriched in mitochondria in human, mouse and rat (PMID:11248059), while the same laboratory later found it almost entirely cytosolic in HeLa with very little mitochondrial colocalisation, and attributed the earlier result to antibody cross-reactivity or cell type (PMID:19797056). This row is accepted because it is the piece of evidence that is independent of that dispute: a mass-spectrometry proteome across HEK293T, HeLa, Huh7 and U2OS, using no AKAP10 antibody at all. The disagreement is real and is recorded as an open knowledge gap rather than resolved by preferring one paper; but a protein can hold a minor mitochondrial pool and a dominant cytosolic pool at once, and both are annotated here. Supporting Evidence: PMID:11248059 Subcellular localization for endogenous mouse, rat, and human D-AKAP2 was determined by immunocytochemistry, immunohistochemistry, and tissue fractionation. D-AKAP2 from all three species is highly enriched in mitochondria. PMID:19797056 Cell fractionation showed that endogenous D-AKAP2 is almost entirely cytosolic |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT transfer from the mouse orthologue, which carries its own IDA plus five HDA rows. Correct for human AKAP10. The node it comes from, however, also delivers this term to two fungal bud-site proteins whose own experimental localisations contradict it - reported as a PAINT issue rather than as a defect in this row. Reason: MGI:MGI:1890218 resolves to two accessions, not one: O88845 AKA10_MOUSE, reviewed Swiss-Prot, 662 aa - the true 1:1 orthologue, same length as the human protein - and Q3TR91, an unreviewed 343 aa TrEMBL fragment carrying zero annotations to this term. The orthologue holds GO:0005739 by IDA (PMID:11248059) plus five HDA rows, so the donor is a genuine experimental source and SOURCE_WEAK_OR_INFERRED would be factually wrong here. PANTHER:PTN001775426 is a tree node, not a protein. The human target has independent human evidence for the same term (the MitoCoP HTP row), so the transfer is not carrying the claim on its own. Accepted. Separately, and not a reason to change this row: PTHR13155 has only six reviewed (Swiss-Prot) members out of 3775 proteins, and node PTN001775426 spans all six, so this mouse-seeded mitochondrion assertion also reaches S. cerevisiae RAX1 - whose own experimental localisations are cellular bud neck, cellular bud scar, plasma membrane, cellular bud tip and fungal-type vacuole, none mitochondrial - and S. pombe rax1, whose only experimental CC is endoplasmic reticulum. That is recorded once in suggested_questions for PAINT. Re-examined for the ORGANELLES project (2026-10-20): PTHR13155-paint.tsv confirms the IBD at PTN001775426 has a single seed, MGI:1890218, whose evidence is organelle-level, so the row can carry no finer location. No sub-compartment is added for AKAP10. The only targeting line is UniProt's predicted transit peptide (1-28, ECO:0000255); no sub-mitochondrial fractionation, protease protection or membrane-association study exists; the organelle itself is contested (PMID:19797056); and a matrix location would sit oddly with a PKA-anchoring role, while outer-membrane association has not been shown. Fewer than two agreeing lines, so the annotation stays at the root. Propagation Review Root cause: NO FAILURE CORE Sources checked: MGI:MGI:1890218 · Mus musculus Akap10 (resolves to UniProtKB:O88845, Swiss-Prot, 662 aa, the 1:1 orthologue; the same MGI id also returns the unreviewed 343 aa fragment Q3TR91, which carries no annotation to this term) SUPPORTS TRANSFER Holds GO:0005739 by its own IDA from PMID:11248059 plus five HDA rows from PMID:14651853 and PMID:18614015. PANTHER:PTN001775426 · PANTHER tree node, not a protein NOT RELEVANT An internal node of PTHR13155 spanning all six reviewed members of the family; unresolvable to a gene product by construction. Supporting Evidence: PMID:11248059 Subcellular localization for endogenous mouse, rat, and human D-AKAP2 was determined by immunocytochemistry, immunohistochemistry, and tissue fractionation. D-AKAP2 from all three species is highly enriched in mitochondria. |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: A third route to the same term, combining Ensembl Compara transfer from mouse Akap10 with the UniProt subcellular-location vocabulary. The term is right, so the row is accepted; what it is not is independent evidence, because it duplicates the IBA row's donor. Reason: UniProtKB:O88845 is the same mouse orthologue that seeds the IBA row, and ensembl:ENSMUSP00000099710 is the Compara-side identifier for that one entry, so the same mouse IDA reaches human AKAP10 through two pipelines. UniProtKB-SubCell:SL-0173 traces to the CC SUBCELLULAR LOCATION Mitochondrion line, which itself carries ECO:0000269|PubMed:11248059, i.e. the same paper again. Accepted rather than demoted, because the term is the same one the HTP and IBA rows carry and splitting the verdict across evidence types for one term would be arbitrary. What is recorded here instead is that the three mitochondrion rows rest on only two underlying observations, one of them disputed, so they should not be counted as three independent supports. Examined for the ORGANELLES project (2026-10-20): the mapping (GO_REF:0000120 combining SL-0173 with the mouse orthologue) records only the organelle, so the root term is the right output; no sub-compartment is supported (see the IBA row). Propagation Review Root cause: NO FAILURE CORE Failure modes: CIRCULAR PROPAGATION Sources checked: UniProtKB:O88845 · Mus musculus Akap10 (Swiss-Prot, 662 aa) - the 1:1 orthologue CIRCULAR OR REDUNDANT Sound in itself, and it does hold GO:0005739 by IDA; redundant here because the same donor already reaches this gene through the PAINT row. ensembl:ENSMUSP00000099710 · Ensembl mouse protein identifier for the same Akap10 entry CIRCULAR OR REDUNDANT The Compara-side identifier for O88845, not a second source. UniProtKB-SubCell:SL-0173 · UniProt controlled-vocabulary subcellular location Mitochondrion CIRCULAR OR REDUNDANT Traces to the same PMID:11248059 observation via the UniProt CC line. |
| GO:0005829 cytosol | IDA GO_REF:0000052 | ACCEPT | Summary: Human Protein Atlas immunofluorescence in human cell lines, and the only human IDA localisation this gene has. Independently corroborated by subcellular fractionation of the endogenous protein. Reason: This is a human assay on human cells, not a transfer, and it agrees with the only other fractionation of endogenous human AKAP10 in the literature, which found the protein almost entirely cytosolic in HeLa with very little colocalisation with mitochondria, endoplasmic reticulum, Golgi, lysosomes or peroxisomes. Given that the protein has no transmembrane segment and no lipid-binding domain, a dominant soluble pool is also what the sequence predicts. Accepted as a real location of the bulk of the protein. Supporting Evidence: PMID:19797056 Cell fractionation showed that endogenous D-AKAP2 is almost entirely cytosolic PMID:19797056 D-AKAP2 showed very little colocalization with markers of the endoplasmic reticulum, the Golgi complex, lysosomes, peroxisomes, or mitochondria |
| GO:0005829 cytosol | TAS Reactome:R-HSA-992708 | ACCEPT | Summary: Sourced from a Reactome reaction whose compartment tag is a property of the reaction, not a measurement of where AKAP10 is. The provenance is weak; the term is independently established, so the row stands. Reason: R-HSA-992708 is "Dual-specific AKAPs bind type I and II PKA regulatory subunits" - a binding reaction, not a localisation experiment. Its cytosol label describes where Reactome places the reaction, which is the same construction that produced spurious cytosol rows on other genes in this campaign, so the check was run here deliberately. The outcome differs from those cases. The term is independently established for this gene by the HPA immunofluorescence IDA and by endogenous cell fractionation (PMID:19797056), so removing or demoting it would act on a provenance technicality against a correct and well-evidenced annotation. Accepted, with the weak sourcing recorded rather than acted on. A null result from a check is still a result. Supporting Evidence: PMID:19797056 Cell fractionation showed that endogenous D-AKAP2 is almost entirely cytosolic |
| GO:0007165 signal transduction | TAS PMID:9326583 D-AKAP2, a novel protein kinase A anchoring protein with a p... | MARK AS OVER ANNOTATED | Summary: The root term of the biological-process signalling branch, asserted from a 1997 paper whose signalling rationale was an explicit speculation about a putative RGS domain. That speculation is contradicted by later work and by residue analysis, and no replacement term exists. Reason: What PMID:9326583 measured is binding of a 40-residue fragment to PKA RI-alpha, RII-alpha and RII-beta. Its signal-transduction framing rested on the RGS domain, which the authors themselves already flagged as divergent: not all of the charged residues conserved in RGS proteins were conserved in D-AKAP2, and they wrote that if it is a functional RGS it may not interact with G-i-alpha as known RGS proteins do. Twelve years later the same group stated the negative outright - no specific interactions with heterotrimeric G proteins and no ability to activate them. Residue analysis in this review (file:human/AKAP10/AKAP10-bioinformatics/RESULTS.md) finds 0 of 5 Galpha transition-state contacts retained in either RGS domain, matching the AXIN1 negative control and unlike the RGS16 and RGS9 positive controls at 5 of 5. Marked over-annotated rather than removed: AKAP10 genuinely is part of cAMP signalling, so the term is not false, merely the uninformative root of the branch. No MODIFY is offered because the natural replacement, GO:0010738 regulation of protein kinase A signaling, was checked and is obsolete; GO has no active term for an AKAP's role in organising PKA signalling. The informative content of this paper is carried by the GO:0034237 rows. Supporting Evidence: PMID:9326583 Surprisingly, not all of the charged residues conserved in RGS proteins reported so far were conserved in D-AKAP2. PMID:9326583 The lack of conservation of these charge residues suggests that if D-AKAP2 is a functional RGS, it may not interact with Giα as most of the known RGSs do, but with other Gα isoforms. PMID:19797056 D-AKAP2 has so far demonstrated no specific interactions with heterotrimeric G proteins, and no ability to activate them, raising the possibility of nontraditional targets. |
| GO:0008104 intracellular protein localization | IBA GO_REF:0000033 | ACCEPT | Summary: The process counterpart of anchoring: an AKAP exists to put another protein somewhere. Correct and core, and the term's apparent vagueness is the right call rather than a granularity defect, because the two donors do genuinely different things at a finer level. Reason: Both protein-level donors carry their own experimental evidence. MGI:MGI:1890218 resolves to O88845, mouse Akap10, Swiss-Prot, 662 aa, which holds GO:0008104 by IDA from PMID:11248059 - the paper that showed in vivo association with PKA in mouse brain and mitochondrial enrichment. SGD:S000005827 resolves to Q08760 RAX1_YEAST, Swiss-Prot, 435 aa, the bud site selection protein, which holds GO:0008104 by two IMP rows from PMID:25416945. Before writing this off as a vague parent, I asked whether the donors agree, because GRANULARITY_MISMATCH only applies when they do. They do not: one localises protein kinase A, the other localises cortical bud-site landmarks. Intracellular protein localization is the genuine least common ancestor of those two, so the general term is the ontology working correctly and no specificity upgrade should be proposed. Accepted as-is. Propagation Review Root cause: NO FAILURE CORE Sources checked: MGI:MGI:1890218 · Mus musculus Akap10 (UniProtKB:O88845, Swiss-Prot, 662 aa) - the 1:1 orthologue SUPPORTS TRANSFER Holds GO:0008104 by IDA from PMID:11248059, its own experimental annotation. PANTHER:PTN001775426 · PANTHER tree node, not a protein NOT RELEVANT Internal node of PTHR13155; not resolvable to a gene product. SGD:S000005827 · Saccharomyces cerevisiae RAX1 (UniProtKB:Q08760, Swiss-Prot, 435 aa), bud site selection protein SUPPORTS TRANSFER Holds GO:0008104 by two IMP rows from PMID:25416945. A distant, architecturally different family member, which is precisely why the shared term sits at this level. |
| GO:0008104 intracellular protein localization | TAS PMID:9326583 D-AKAP2, a novel protein kinase A anchoring protein with a p... | ACCEPT | Summary: The same term from the original 1997 description. The paper demonstrated R-subunit binding rather than localisation, so the localisation statement is an inference from what anchoring means - sound, but second-hand relative to the IBA row. Reason: PMID:9326583's experiments are coprecipitation assays mapping a 40-residue fragment onto the N-terminal dimerization domains of RI-alpha and RII-alpha, plus Northern blots and in situ hybridisation. No localisation of PKA by D-AKAP2 was measured in that paper; the localisation claim follows from the definition of an anchoring protein. Accepted anyway, for two reasons. The conclusion is correct and is independently carried by the IBA row, whose mouse donor did test in vivo PKA association. And the term is the same one that row carries, so giving the two rows different verdicts would record a judgement about provenance as though it were a judgement about the biology. Supporting Evidence: PMID:9326583 Based on coprecipitation assays, the R binding domain interacts with the N-terminal dimerization domain of RIalpha and RIIalpha. |
| GO:0016020 membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Derived from the Membrane entry in UniProt's subcellular-location line, which is itself experimentally sourced. Kept, but AKAP10 has no transmembrane segment and no lipid-binding domain, so how it attaches to any membrane is unresolved. Reason: UniProt's CC SUBCELLULAR LOCATION line lists Membrane with ECO:0000269|PubMed:11248059 and notes that the protein is predominantly mitochondrial but also membrane-associated and cytoplasmic, so the term is not invented by the mapping rule. Held non-core for two reasons. First, GO:0016020 is the root of the membrane branch and names no compartment. Second, the feature table contains no TRANSMEM feature and no lipid-binding domain, and the ternary-complex paper states that, unlike many AKAPs, D-AKAP2 does not contact the membrane protein directly - it reaches transporters through a PDZ scaffold. So any membrane association is peripheral and indirect, which a bare located_in does not convey. Supporting Evidence: PMID:25348485 In contrast to many other AKAPs, D-AKAP2 does not interact directly with the membrane protein. |
| GO:0032991 protein-containing complex | IDA PMID:25097019 A systematic evaluation of protein kinase A-A-kinase anchori... | KEEP AS NON CORE | Summary: True but maximally uninformative: the root of the complex branch, recording that AKAP10 forms a complex with a PKA regulatory subunit. GO has no term for an AKAP-anchored PKA assembly, so there is nothing to modify to. Reason: Querying QuickGO by reference shows PMID:25097019 contributes 26 annotations over 8 distinct entities, with GO:0032991 given by IDA to all 8 - the shape of a projection. It is benign in this case: each of the 8 AKAPs in that study was individually assayed by fluorescence anisotropy, so this is parallel per-protein curation rather than one phenotype distributed across a complex's membership. The row is therefore kept on its evidence and demoted on informativeness, not on provenance. No replacement is offered because none exists. GO:0005952 cAMP-dependent protein kinase complex was checked and is defined strictly as the regulatory-plus-catalytic holoenzyme, which AKAP10 is not a subunit of, and it has no children. An OLS search of GO for AKAP and for "A-kinase anchoring protein complex" returns nothing; since ontology search is token-based that is not proof of absence, so the observation is filed as a question for GO rather than as a proposed term. Supporting Evidence: PMID:25097019 To verify the validity of these newly predicted anchoring sites and their putative specificities, we used computational modeling approaches (HADDOCK), biochemical affinity studies (fluorescence anisotropy), and cellular colocalization studies. |
| GO:0043495 protein-membrane adaptor activity | IBA GO_REF:0000033 | ACCEPT | Summary: The anchoring activity itself, transferred from the mouse orthologue's own IDA. This is what an AKAP is for, and it is the only GO molecular function that expresses tethering rather than mere binding. Reason: The donor MGI:MGI:1890218 resolves to O88845, mouse Akap10, Swiss-Prot, 662 aa, which holds GO:0043495 by IDA from PMID:11248059 - the study that demonstrated in vivo association of D-AKAP2 with PKA in mouse brain by cAMP-agarose pull-down and placed the endogenous protein in mitochondria in three species including human. So the transfer rests on a real experimental annotation, not on a further inference. GO:0043495 is also the most specific fit available. Its ten children are all of the form cargo-plus-membrane anchor activity and none covers a kinase, and there is no A-kinase-anchoring molecular function anywhere in GO. Accepted as core, with the caveat recorded elsewhere that the membrane-attachment mechanism of this particular AKAP is unresolved. Propagation Review Root cause: NO FAILURE CORE Sources checked: MGI:MGI:1890218 · Mus musculus Akap10 (UniProtKB:O88845, Swiss-Prot, 662 aa) - the 1:1 orthologue SUPPORTS TRANSFER Holds GO:0043495 by IDA from PMID:11248059, assigned by GO_Central. PANTHER:PTN001775426 · PANTHER tree node, not a protein NOT RELEVANT Internal node of PTHR13155; not resolvable to a gene product. Supporting Evidence: PMID:11248059 In vivo association of D-AKAP2 with PKA in mouse brain was demonstrated by using cAMP agarose pull-down assay. |
| GO:0043495 protein-membrane adaptor activity | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl Compara transfer of the same mouse IDA that seeds the IBA row. The activity is real and core, so the row is accepted; it simply is not a second piece of evidence. Reason: UniProtKB:O88845 and ensembl:ENSMUSP00000099710 are two identifiers for one mouse entry, and that entry's only experimental support for this term is the single IDA from PMID:11248059 that the PAINT row already uses. Accepted because the activity it asserts is the gene's defining one and the same term is accepted on the IBA row; recorded here so that the two rows are not counted as two independent supports for the anchoring function. Propagation Review Root cause: NO FAILURE CORE Failure modes: CIRCULAR PROPAGATION Sources checked: UniProtKB:O88845 · Mus musculus Akap10 (Swiss-Prot, 662 aa) - the 1:1 orthologue CIRCULAR OR REDUNDANT Sound, and it does hold GO:0043495 by IDA, but it is the same donor and the same single experiment that the IBA row already transfers. ensembl:ENSMUSP00000099710 · Ensembl protein identifier for the same mouse Akap10 entry CIRCULAR OR REDUNDANT The Compara-side identifier for O88845, not a second source. |
| GO:0051018 protein kinase A binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from IPR037719, the AKAP10 A-kinase-binding domain. The domain binds the regulatory subunit specifically, so the mapping can be one level more precise than it is. Reason: IPR037719 is AKAP10_AKB_dom, the family-specific signature for exactly the segment that UniProt annotates as "FT REGION 634..647" with note PKA-RII subunit binding and that PDB 3IM4 resolves as a helix on the RI-alpha dimerization/docking domain. A family-specific signature of a characterised binding module is much better founded than a bare fold signature, so this row is not in doubt - only its granularity is. Every structure and every affinity measurement involving this domain, across AKAP10 and the wider AKAP family, is against an R subunit; the AKB helix has no reported affinity for the catalytic subunit, and the two PDB chains cross-referenced from this entry are both R-subunit complexes. GO:0034237 protein kinase A regulatory subunit binding is an active child of GO:0051018 and is what the signature actually predicts. Re-pointing this one interpro2go line would fix every AKAP10 orthologue at once, which is the kind of upstream fix worth making rather than patching gene by gene. Proposed replacements: protein kinase A regulatory subunit binding Supporting Evidence: PMID:25097019 The regulatory subunits of the four PKA isoforms (RIα, RIβ, RIIα, and RIIβ) each form a homodimer, and their dimerization domain interacts with a small helical region present in each of the more than 40 AKAPs reported so far. |
| GO:0051018 protein kinase A binding | IPI PMID:25097019 A systematic evaluation of protein kinase A-A-kinase anchori... | MODIFY | Summary: Direct affinity measurement against human PKA RI-alpha by fluorescence anisotropy. Real, human, and core - but it measured the regulatory subunit, and GO has a child term that says so. Reason: P10644 resolves to KAP0_HUMAN, reviewed Swiss-Prot, 381 aa - canonical human PRKAR1A, so this is a human protein assayed against a human partner and IPI is the correct code. The assay is fluorescence anisotropy on the AKAP10 anchoring helix, backed in the same study by HADDOCK modelling and cellular colocalisation. GO:0051018's own comment notes that it spans binding to either the catalytic or the regulatory subunit. Nothing in the AKAP10 literature assays the catalytic subunit, and all three structural studies of this protein are R-subunit complexes, so the parent term understates what is known. GO:0034237 protein kinase A regulatory subunit binding is exact. Proposed replacements: protein kinase A regulatory subunit binding Supporting Evidence: PMID:25097019 To verify the validity of these newly predicted anchoring sites and their putative specificities, we used computational modeling approaches (HADDOCK), biochemical affinity studies (fluorescence anisotropy), and cellular colocalization studies. PMID:20159461 Dual-specific AKAP 2 (D-AKAP2) binds to the dimerization/docking (D/D) domain of both RI and RII regulatory subunits of PKA with high affinity. |
| GO:0051018 protein kinase A binding | IPI PMID:25097019 A systematic evaluation of protein kinase A-A-kinase anchori... | MODIFY | Summary: The type II half of the dual specificity, the same anchoring helix measured against human PKA RII-alpha. Same term change as the RI-alpha row. Reason: P13861 resolves to KAP2_HUMAN, reviewed Swiss-Prot, 404 aa - canonical human PRKAR2A. Note that this partner has no IntAct record at all, so the annotation comes from UniProt's direct curation of the paper rather than from an interaction database; that is a difference in provenance, not a weakness in the evidence. This row is what makes AKAP10 dual-specific rather than a conventional RII-only AKAP, a property established in the original description - the active fragment bound RI-alpha, RII-alpha and RII-beta but not RI-beta - and later explained structurally by a shift in the helical register between the RI and RII complexes. As with the RI-alpha row, only the regulatory subunit was assayed, so GO:0034237 is the correct term. Proposed replacements: protein kinase A regulatory subunit binding Supporting Evidence: PMID:20159461 An unexpected shift in the helical register of D-AKAP2 compared to the RIIalpha:D-AKAP2 complex structure makes the mode of binding to RIalpha novel. PMID:25097019 To verify the validity of these newly predicted anchoring sites and their putative specificities, we used computational modeling approaches (HADDOCK), biochemical affinity studies (fluorescence anisotropy), and cellular colocalization studies. |
| GO:0031267 small GTPase binding | IPI PMID:19797056 D-AKAP2 interacts with Rab4 and Rab11 through its RGS domain... | NEW | Summary: Proposed. AKAP10's tandem RGS domains bind Rab11 and GTP-loaded Rab4, acting as a single functional unit. This was the first report of RGS domains binding small GTPases, and GO records nothing about it on any gene. Reason: The experiments are on the human protein in human cells, which the paper states explicitly - all D-AKAP2 constructs used the human gene - so IPI rather than ISS is the correct code for the AKAP10 side. Four independent assays: co-immunoprecipitation from HEK293 cells, which pulls down Rab4 and Rab11 but not Rab5; a GST-Rab4 pull-down showing the interaction is nucleotide-state dependent, with GTP-gamma-S-loaded Rab4 far more effective than GDP-loaded Rab4 or GST alone; split-ubiquitin yeast two-hybrid with the isolated tandem domains; and colocalisation of the endogenous protein with Rab4 and Rab11 on endosomes. The binding surface is mapped and the mapping is informative. Residues 120-513, spanning both RGS domains, are necessary and sufficient, while neither RGS-A nor RGS-B alone binds either Rab. So the two divergent RGS domains that are not Galpha GAPs have a joint function as a small-GTPase-binding module. Term choice checked rather than assumed. GO:0017137 Rab GTPase binding has been merged into GO:0031267, which QuickGO confirms by listing GO:0017137 among its secondaryIds, and GO:0031267 has no children. It is therefore already maximal and no substrate-specific child should be proposed; the identity of the Rabs is recorded machine-readably with has_input extensions instead. One honesty note on partner species. The tagged Rab constructs are described as canine Rab4b and the Rab11a construct's origin is not stated, so the extensions name the human orthologues as the biologically intended inputs rather than claiming a human-human interaction was measured in every assay. The endogenous colocalisation in Fig. 3C-E is with Rab proteins in human HeLa cells. Supporting Evidence: PMID:19797056 We show here that these RGS domains interact with Rab11 and GTP-bound Rab4, the first demonstration of RGS domains binding small GTPases. PMID:19797056 D-AKAP2 specifically co-immunoprecipitated GFP-tagged Rab4 and Rab11 but not Rab5. PMID:19797056 Furthermore, purified GST-tagged Rab4 bound to the nonhydrolyzable nucleotide analog GTPγS was much more able to pull down D-AKAP2 from a HEK293 lysate than GDP-bound GST-Rab4 or GST alone PMID:19797056 Neither RGS-A (residues 120–369) nor RGS-B (residues 374–513) alone was able to interact with Rab4 or Rab11, suggesting that the two RGS domains form a single functional unit. PMID:19797056 All D-AKAP2 constructs used the human gene with valine at position 646. |
| GO:2001136 negative regulation of endocytic recycling | IMP PMID:19797056 D-AKAP2 interacts with Rab4 and Rab11 through its RGS domain... | NEW | Summary: Proposed. Depleting AKAP10 from human cells makes transferrin recycle 73 percent faster and pushes Rab11 and the transferrin receptor to the cell periphery, so the wild-type protein slows traffic out of the recycling compartment. Reason: Human siRNA in HeLa cells knocking down the endogenous human protein, so IMP is the correct code and the species is unambiguous. The readout is quantitative. After a 20 min pulse the knockdown cells retain 33.3 percent more transferrin (p = 0.0022) and after a 30 min chase 31.0 percent less (p = 0.023), and fitting the whole series gives a recycling rate 73 percent faster than control. Morphologically, Rab11 and the endogenous transferrin receptor both redistribute toward the periphery while EEA1-marked early endosomes are unchanged, so the effect is specific to the recycling compartment. Direction checked explicitly, because this is exactly where a regulation term can be inverted. Loss of the protein accelerates recycling, therefore the protein normally restrains it, therefore the negative-regulation term. GO:2001136 is active and its definition - any process that stops, prevents or reduces the frequency, rate or extent of endocytic recycling - matches. The positive-regulation sibling GO:2001137 would assert the opposite of the data. Supporting Evidence: PMID:19797056 Treating HeLa cells for 2 days with siRNA directed against D-AKAP2 effectively knocked down nearly all of the endogenous protein PMID:19797056 Fitting all of the data to an exponential decay function yielded a rate of transferrin recycling that was 73 ± 21% faster in the D-AKAP2 knockdown cells than in control cells PMID:19797056 These results suggest that endogenous D-AKAP2 may promote the accumulation of transferrin in the slow recycling pathway of the Rab4/Rab11-containing ERC. |
| GO:0055037 recycling endosome | IDA PMID:19797056 D-AKAP2 interacts with Rab4 and Rab11 through its RGS domain... | NEW | Summary: Proposed. A pool of AKAP10 sits on Rab4/Rab11-positive recycling endosomes. The bulk of the protein is cytosolic, so this is a minor but functionally decisive pool - it is where the Rab binding and the recycling phenotype happen. Reason: Recorded as IDA on the strength of the endogenous-protein experiment. Endogenous AKAP10, visualised with a monoclonal antibody, colocalises with Rab4 and Rab11 on endosomes and prefers endosomes positive for both. Supporting images with tagged protein show colocalisation with pulse-chased fluorescent transferrin and with the endogenous transferrin receptor. The caveat is stated rather than buried. The endosomal pool is a minority against a dominantly cytosolic background, and co-expression of Rab4 or Rab11 increases it, so the clearest images involve overexpressed Rab. That is why the row is GO:0055037 located_in rather than a stronger is_active_in claim, and it is consistent with, not contradicted by, the cytosol IDA row. Supporting Evidence: PMID:19797056 Endogenous D-AKAP2 also clearly colocalized with GFP-Rab4 and mCh-Rab11 on endosomes, with an apparent preference for endosomes positive for both Rab proteins PMID:19797056 D-AKAP2 in these puncta colocalized significantly with internalized fluorescently labeled transferrin, a marker of the endocytic recycling pathway |
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Download this section (compressed HTML)Q: Should the InterPro2GO line for IPR037719 be re-pointed from GO:0051018 protein kinase A binding to GO:0034237 protein kinase A regulatory subunit binding? IPR037719 is the family-specific signature for the AKAP10 A-kinase-binding domain, which UniProt annotates as PKA-RII subunit binding and which both cross-referenced PDB entries resolve bound to an R subunit. No experiment on AKAP10, or on the AKB helix of any AKAP, assays the catalytic subunit. Fixing the mapping once would correct every AKAP10 orthologue rather than one gene.
Suggested experts: InterPro curator, GO molecular function editor
Q: PAINT node PTN001775426 in PTHR13155 asserts GO:0005739 mitochondrion with is_active_in from a single mouse seed (MGI:MGI:1890218), and the node spans all six reviewed members of the family. Three of those six are not AKAPs: Saccharomyces cerevisiae RAX1 (Q08760), Schizosaccharomyces pombe rax1 (Q9P7S8) and Caenorhabditis elegans rgs-5 (Q10955). RAX1's own experimental localisations are cellular bud neck, cellular bud scar, plasma membrane, cellular bud tip and fungal-type vacuole; pombe rax1's only experimental CC is endoplasmic reticulum. Should the mitochondrion assertion move to a node whose reach is the mammalian AKAP10 orthologues, leaving GO:0008104 - which both the mouse and the yeast donors independently support - at the family node? The GO:0043495 assertion has the same scope question. Affected genes named in full so the fix can be made once.
Suggested experts: PAINT curator, GO_Central
Q: GO cannot express what an AKAP does. GO:0051018 and GO:0034237 say only that the protein binds the kinase, and GO:0043495 requires a membrane, which excludes the AKAPs that anchor to the cytoskeleton or centrosome. Searching GO for AKAP and for "A-kinase anchoring protein complex" returns nothing, and GO:0005952 cAMP-dependent protein kinase complex is defined strictly as the regulatory-plus-catalytic holoenzyme, so the AKAP-anchored assembly this gene demonstrably forms can only be annotated to GO:0032991, the root. Ontology search is token-based so a null query is not proof of absence, hence a question rather than a proposed term. Would GO consider either a kinase-anchoring molecular function or a complex term for the AKAP-PKA assembly? More than forty human AKAPs would use it.
Suggested experts: GO ontology editor
Q: Is human AKAP10 mitochondrial? The gene's UniProt name says so, on the strength of immunocytochemistry and fractionation of endogenous protein from three species (PMID:11248059), and the protein is in the MitoCoP high-confidence mitochondrial proteome. But the same laboratory later found endogenous protein almost entirely cytosolic in HeLa with very little mitochondrial colocalisation, and attributed the earlier result to antibody cross-reactivity or cell type (PMID:19797056). The transit peptide is predicted, not measured, and there is no transmembrane segment. Both localisations are annotated here; a curator with access to current reagents could settle which pool dominates in which cell type.
Suggested experts: mitochondrial cell biologist, GOA curator
Q: Why has no annotation anywhere in GOA been made from PMID:19797056? QuickGO returns zero results for that reference across all species and all genes, yet it reports the first demonstration of RGS domains binding small GTPases, maps the binding surface, and quantifies a recycling phenotype by siRNA in human cells. Three NEW rows are proposed here from it; the partner genes RAB4A, RAB11A and TFRC would also gain from it.
Suggested experts: GOA curator
Q: Should the association between the common AKAP10 I646V variant and heart-rate phenotypes be represented anywhere in GO? It is deliberately not annotated here: the perturbation experiments are in mouse, the mouse allele is dominant-interfering rather than a clean null, and the human evidence is a population association, so it describes neither a molecular function nor a process of the wild-type protein. Confirmation that this is the right call, and a pointer to where such an association should live instead, would be useful.
Suggested experts: GOA curator, cardiovascular geneticist
Experiment: Reconstitute AKAP10-knockdown HeLa cells with wild-type protein, with an anchoring-dead mutant of the 629-653 helix, and with the PDZ-motif deletion construct, then measure transferrin recycling rate by the published flow-cytometry pulse-chase. If only the wild type restores the restraint on recycling, the anchored kinase is part of the recycling mechanism; if the anchoring-dead mutant rescues fully, the RGS and AKB arms are independent modules.
Hypothesis: The PKA-anchoring arm and the Rab-binding arm of AKAP10 are one coupled mechanism rather than two independent modules sharing a polypeptide.
Type: rescue with separation-of-function mutants plus flow-cytometry recycling assay
Experiment: Knock a fluorescent tag into the endogenous AKAP10 locus in a cell line where the mitochondrial claim was originally made and in HeLa, then quantify the mitochondrial and cytosolic pools by live imaging and by proximity labelling from a matrix-targeted and an outer-membrane-targeted bait. This removes the antibody-specificity variable that the two conflicting studies disagree about.
Hypothesis: The disagreement between the mitochondrial and cytosolic localisation reports is an antibody-specificity artefact rather than a genuine difference in the protein's distribution.
Type: endogenous fluorescent knock-in imaging plus compartment-specific proximity labelling
Experiment: Perform in organello import of radiolabelled full-length AKAP10 into isolated human mitochondria with and without membrane potential, with and without protease treatment, and determine by N-terminal sequencing whether residues 1-28 are cleaved. This distinguishes a genuine targeting sequence from a prediction artefact and would explain the topology.
Hypothesis: The predicted N-terminal transit peptide is not a functional matrix-targeting sequence, since a protein that anchors cytosolic PKA cannot be imported into the matrix.
Type: in organello mitochondrial import assay
Experiment: Assay purified AKAP10 RGS-A, RGS-B and the tandem construct for single-turnover GTP hydrolysis acceleration against a panel of Galpha subunits spanning the i, q, s and 12/13 families, with RGS4 as the positive control. A clean negative across the panel would convert a well-supported inference into a citable measurement and justify a NOT annotation.
Hypothesis: Neither AKAP10 RGS domain accelerates GTP hydrolysis by any heterotrimeric G-protein alpha subunit, as the absence of the Galpha transition-state contact residues predicts.
Type: single-turnover GTP hydrolysis assay against a Galpha panel
Experiment: Solve or predict-and-validate the complex between AKAP10 residues 120-513 and GTP-loaded Rab4, then test switch-region mutants of Rab4 for loss of binding. Because this is the only reported case of RGS domains binding small GTPases, the structural basis would say whether the Galpha-binding surface has been repurposed or a different face of the fold is used.
Hypothesis: The tandem RGS module engages Rab4 through the switch regions, i.e. the same face an RGS box uses on Galpha has been repurposed for a small GTPase.
Type: structure determination plus switch-region mutagenesis
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