A0A8B6GS20 (ORF MGAL_10B089004) is a partial gene model from the Mediterranean mussel genome. Its C-terminal 246 residues belong to a myotubularin-related protein 9 (MTMR9)-type pseudophosphatase, placed in PANTHER subfamily PTHR10807:SF73 with Caenorhabditis elegans MTM-9. Its first ~360 residues are three D8C_UMOD-like cysteine-rich repeats of a kind found in extracellular proteins and unrelated to myotubularins. The retained myotubularin region covers only the C-terminal half of the phosphatase-like domain and the C-terminal region. It carries the MTMR9-type inactive site, with glycine at the catalytic cysteine position of the CX5R motif and threonine at the arginine position. The PH-GRAM domain and the N-terminal half of the phosphatase-like fold are absent. A full-length MTMR9-type model (ORF MGAL_10B079678) exists in the same genome and is 97% identical over the shared region. MTMR9-family proteins are catalytically inactive partners of active myotubularin 3-phosphatases (MTMR6/7/8 in mammals, MTM-6 in nematodes). They bind the active partner, stabilise it and raise its phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate 3-phosphatase output in the cytoplasm. Through that complex they act in endosomal trafficking. No experiments have been reported for the mussel protein, and the product encoded by this particular model is unlikely to fold as a complete MTMR9 protein.
Summary: TreeGrafter transfer from the MTMR9 clade node PANTHER:PTN000086907. MTMR9-family proteins are cytoplasmic, membrane-associated partners of active myotubularins. In the mammalian studies they relocalise with active partners, and in C. elegans MTM-9 acts with MTM-6 in endocytic traffic. The A0A8B6GS20 model carries extracellular-type D8C_UMOD repeats at its N-terminus, which probably come from a gene-model fusion and do not argue against cytoplasmic localisation of the mussel MTMR9 gene product. Cytoplasm is as precise as the phylogenetic evidence allows for this species.
Reason: Cytoplasmic localisation is conserved across the MTMR9 clade. That clade includes the worm protein in this PANTHER subfamily (SF73), and the endocytic-pathway work places MTM-9 in the cytoplasm. The target's MTMR9-homologous region is the clade member. Gene-model caveat: the N-terminal D8C_UMOD region of this model is not part of an MTMR9 protein.
Summary: The underlying IBA rests on one donor, human MTMR9. In human cells the MTMR8-MTMR9 complex lowered PtdIns(3)P and inhibited autophagy. The node placement is a legitimate PAINT judgement and is not challenged on donor count. The biology behind it is narrower than the clade, though. The autophagy effect was shown for the pairing with MTMR8, a member of the vertebrate MTMR6/7/8 expansion. Invertebrates have a single MTM-6-type partner, and the C. elegans MTM-6/MTM-9 work describes endocytic traffic and Wnt-carrier recycling, not autophagy. It is a regulatory outcome of the partner phosphatase's PtdIns(3)P turnover, so it sits downstream of the core activity.
Reason: The term is supported for vertebrate MTMR9 with MTMR8. For a mollusc it is a plausible but untested regulatory consequence of partner-phosphatase activation. It is peripheral to the core function, which is partner binding and activation of a 3-phosphatase. The fragmentary gene model adds uncertainty for this accession.
the MTMR8/R9 complex reduces cellular PtdIns(3)P levels. Consequentially, the MTMR6/R9 complex serves to inhibit stress-induced apoptosis and the MTMR8/R9 complex inhibits autophagy.
We conclude that regulation of endosomal trafficking by the MTM-6/MTM-9 myotubularin complex is required for the retromer-dependent recycling of MIG-14/Wls and Wnt secretion.
Summary: Partner binding is the central activity of MTMR9-family proteins. They heterodimerise with active myotubularins (MTMR6, MTMR7 and MTMR8 in human; MTM-6 in C. elegans). Those partners are lipid 3-phosphatases acting on PtdIns(3)P and PtdIns(3,5)P2, not phosphoprotein phosphatases. GO:0019903 is defined as binding to a protein phosphatase, so the bound partner does not strictly fit it. The parent term phosphatase binding (GO:0019902) describes the interaction accurately. The human MTMR9 review left the same partner-class question UNDECIDED. The target keeps the C-terminal region of MTMR9 (human residues 313-542), so the region needed for partner association is plausibly present even in this partial model.
Reason: The interaction is real and core, but the partner is a lipid phosphatase, so the right level is the parent GO:0019902 phosphatase binding. Phosphatase activator activity (GO:0019211, human EXP) was not propagated by PAINT to the clade node and is not proposed here.
Summary: PAINT placed this process at the active ancestral node PTN008506586. At the MTMR9 clade node PTN000086907 the curators negated only the catalytic activities, recording loss of phosphatidylinositol-3-phosphate phosphatase activity (GO:0004438) and phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0106018) as IRD rows. They did not negate the process, so the retained process is a deliberate decision. Biologically, MTMR9 is the noncatalytic subunit of the heteromeric phosphatase: it raises partner activity up to 30-fold toward PtdIns(3,5)P2 and fixes substrate preference. That is the scaffold/regulatory-subunit kind of participation that justifies a process annotation for a noncatalytic complex member. The worm MTM-6/MTM-9 complex is described as acting to dephosphorylate PtdIns(3)P. The target has the same MTMR9-type inactive site (Gly at the Cys position, Thr at the Arg position), so it has no intrinsic catalysis.
Reason: MTMR9-family proteins do part of the work of this process as obligate regulatory subunits of the active 3-phosphatase complex. PAINT deliberately retained the process while negating the activities at this node. This review accepts it; the earlier review proposed replacing it with regulation of phosphatidylinositol dephosphorylation. Gene-model caveat: this accession lacks the N-terminal half of the MTMR9 fold.
So the retained region has the MTMR9-type inactive site.
Core Functions
Noncatalytic MTMR9-type subunit of a myotubularin phosphatase complex. It binds an active myotubularin 3-phosphatase, stabilises it and raises its activity toward phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate in the cytoplasm. This is inferred for the mussel MTMR9 gene from PANTHER subfamily SF73 (with C. elegans MTM-9) and from the conserved MTMR9-type inactive site. This partial gene model keeps only the C-terminal ~45% of the protein.
Q: Is MGAL_10B089004 a haplotig-derived partial copy of the MTMR9 gene MGAL_10B079678, or a real partial duplicate fused to D8C_UMOD exons? If it is an assembly or annotation artefact, should UniProt merge or flag the entry?
Q: PANTHER places C. elegans MTM-9 and this mussel protein in SF73 and vertebrate MTMR9 in SF56. Is the split only taxonomic, or does it mark a functional difference in partner choice (single MTM-6-type partner vs the vertebrate MTMR6/7/8 set)?
Suggested Experiments
Experiment: Use RT-PCR or long-read transcript evidence across the junction between the D8C_UMOD repeats and the MTMR9 region of MGAL_10B089004 to find out whether a fused transcript exists in mussel tissues.
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 (UniProt 2024_06 pilot) emitted one GO prediction for this partial MTMR9-type gene model, phosphatidylinositol-3-phosphate phosphatase activity (GO:0004438). It is refuted: the retained phosphatase-like region carries the MTMR9-type inactive site (Gly and Thr at the catalytic Cys and Arg positions), the protein sits in PANTHER subfamily SF73 with the phosphatase-inactive C. elegans MTM-9, and PAINT negates this activity at the MTMR9 clade node.
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
PSEUDOENZYME OVERANNOTATION
Review rationale: The prediction is an intrinsic lipid 3-phosphatase activity, which is not among the gene's GOA annotations. A0A8B6GS20 is a partial MTMR9-type gene model whose myotubularin-like region (residues 362-607) aligns to the C-terminal part of human MTMR9 and is placed in PANTHER PTHR10807:SF73 with C. elegans MTM-9, which is described experimentally as phosphatase-inactive. The retained CX5R-equivalent P-loop reads VHGSEGFDTT, with Gly at the catalytic Cys position and Thr at the Arg position, the same kind of substitution seen in human MTMR9 and worm MTM-9. PAINT records the loss of GO:0004438 (and GO:0106018) by IRD NOT rows at the MTMR9 clade node PTN000086907, and the gene review treats the protein as a noncatalytic regulatory subunit that binds and activates an active myotubularin partner. MTMR9-family proteins raise partner 3-phosphatase output without catalysis themselves (PMID:22647598), so participation in phosphatidylinositol dephosphorylation is supported while the predicted intrinsic activity is not. This is a catalytic activity transferred to a fold-retaining pseudophosphatase.
Supporting Evidence:
file:MYTGA/A0A8B6GS20/A0A8B6GS20-uniprot.txt: "ID A0A8B6GS20_MYTGA Unreviewed; 607 AA. ... DR InterPro; IPR010569; Myotubularin-like_Pase_dom. ... DR PANTHER; PTHR10807:SF73; LD06050P; 1. ... DR PANTHER; PTHR10807; MYOTUBULARIN-RELATED; 1. ... FT DOMAIN 372..544 ... FT /note="Myotubularin phosphatase""
PMID:22647598: "inactive because they lack the conserved cysteine residue"
file:MYTGA/A0A8B6GS20/A0A8B6GS20-bioinformatics/RESULTS-rereview.md: "The target has Gly at the Cys position and Thr at the Arg position. Human MTMR9 (IHGTEGTDST) and worm MTM-9 (IHGGDGLDST) carry the same kind of substitution. So the retained region has the MTMR9-type inactive site."
PMID:14565969: "the phosphatase-inactive MTM-9 protein is also predominantly localized to the coelomocyte cytoplasm"