LMTK3 is a single-pass membrane protein serine/threonine kinase with a membrane-proximal catalytic domain that phosphorylates protein substrates including RAB7A, HSPB1, CDC37, and ESR1. In human cell models it regulates endosomal cargo transport through RAB11FIP1-RAB14-EPHA2 and RAB7A pathways, and a nuclear pool binds PPP1CA/PP1alpha to scaffold TRIM28/KAP1 dephosphorylation and transcriptional repression. LMTK3 also sustains ESR1 abundance and signaling in estrogen-receptor-positive breast-cancer cells. Neuronal receptor-trafficking and KCC2-linked PP1-scaffold roles are established primarily in rodents and remain unverified in human neurons.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004672 protein kinase activity | IBA GO_REF:0000033 | MODIFY | Summary: The PAINT annotation correctly recognizes a conserved LMTK-family protein kinase, but the parent term is less informative than direct human enzymology. Purified LMTK3 phosphorylates serine/threonine-containing peptide substrates, and RCP Ser435 is a defined cellular substrate. Reason: Replace generic protein kinase activity with the experimentally established protein serine/threonine kinase activity. The family transfer itself is sound; the problem is only term granularity at the target, where direct biochemical evidence resolves the specificity. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: MGI:MGI:1197518 · mouse Lmtk1/Aatk SUPPORTS TRANSFER The related mammalian LMTK-family kinase supports the conserved parent activity. PANTHER:PTN004704357 · PANTHER ancestral node SUPPORTS TRANSFER The ancestral node supports kinase activity across this LMTK clade. UniProtKB:Q8IWU2 · human LMTK2 SUPPORTS TRANSFER LMTK2 is an experimentally characterized serine/threonine protein kinase. UniProtKB:Q96Q04 · human LMTK3 target SUPPORTS TRANSFER Self-reference: the target is its own IBD seed, which is expected rather than circular -- its own EXP annotation to GO:0106310 (protein serine kinase activity), a descendant of this term, is one of the descendant evidences behind the IBD. The IBA then asserts the additional claim that the function is inherited rather than lineage-specific. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:28294115 Phosphorylation of RCP at Ser435 by Lemur tyrosine kinase-3 (LMTK3) and of EphA2 at Ser897 by Akt are both necessary to promote Rab14-dependent (and Rab11-independent) trafficking of EphA2 which generates cell:cell repulsion events that drive tumour cells apart. |
| GO:0000139 Golgi membrane | IEA GO_REF:0000044 | ACCEPT | Summary: The automatic row faithfully maps the current UniProt Golgi-apparatus-membrane statement. That statement is transferred from experimentally localized mouse Lmtk3 (Q5XJV6), rather than measured directly for human Q96Q04. Reason: Golgi membrane localization is conserved and biologically coherent with LMTK3's membrane-trafficking functions. Accept with the explicit caveat that the human annotation is orthology-based, not direct human localization evidence. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0134 · UniProtKB Golgi apparatus membrane vocabulary term SUPPORTS TRANSFER The mapping is accurate; the underlying human UniProt statement is based on similarity to mouse Lmtk3 Q5XJV6. |
| GO:0004672 protein kinase activity | IEA GO_REF:0000002 | MODIFY | Summary: The InterPro mappings correctly identify a protein kinase domain but assign only the generic parent activity. Direct assays of human LMTK3 resolve serine/threonine phosphotransferase activity. Reason: Replace the broad domain-level term with GO:0004674. The source signatures support a kinase fold, while target-specific biochemical evidence supplies the more informative substrate-residue specificity. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: InterPro:IPR001245 · serine/threonine/tyrosine protein kinase catalytic domain SUPPORTS TRANSFER The domain supports kinase activity but maps more broadly than the human assays. InterPro:IPR008266 · tyrosine kinase active-site signature SUPPORTS TRANSFER The sequence signature supports the kinase fold, not target residue specificity. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:33188023 Radiolabeled biochemical assays using a positional scanning peptide library (PSPL) (18) resulted in elucidation of the LMTK3 phosphorylation consensus sequence and the subsequent identification of heat shock protein 27 (HSP27) as an in vitro phosphorylation substrate of LMTK3. |
| GO:0004674 protein serine/threonine kinase activity | IEA GO_REF:0000003 | ACCEPT | Summary: Correct core molecular function. The EC mapping is independently corroborated by purified-domain peptide phosphorylation assays and by LMTK3-dependent phosphorylation of RCP at Ser435. Reason: EC 2.7.11.1 is the appropriate activity class for the experimentally active human LMTK3 kinase domain. Both direct enzymology and a defined serine substrate support the assignment. Propagation Review Root cause: NO FAILURE CORE Sources checked: EC:2.7.11.1 · non-specific serine/threonine protein kinase SUPPORTS TRANSFER The EC assignment matches direct human LMTK3 biochemical evidence. Supporting Evidence: PMID:28294115 Here, we identify a novel pathway in which a transmembrane serine/threonine kinase (LMTK3) phosphorylates a Rab effector (RCP) to control EphA2 trafficking. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: ATP binding is supported by the conserved active-site structure and ATP-dependent phosphotransfer assays, but it is a generic mechanistic feature beside the catalytic kinase terms. Reason: Retain as a correct non-core molecular feature. The ATP-binding-site signature and structure support the annotation, while protein serine/threonine kinase activity is the biologically informative core function. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: InterPro:IPR000719 · protein kinase domain SUPPORTS TRANSFER The kinase domain supports ATP use, but the separate binding term is generic. InterPro:IPR017441 · protein kinase ATP-binding-site signature SUPPORTS TRANSFER The signature directly supports ATP binding in the catalytic domain. Supporting Evidence: PMID:33188023 Together, the features of the LMTK3 kinase domain indicate that the critical residues required for its binding and hydrolysis of ATP are conserved (fig. S1). |
| GO:0016020 membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Broad membrane localization is consistent with the annotated N-terminal signal peptide and single transmembrane helix and with experimentally studied membrane-trafficking roles of LMTK3. Reason: Membrane association is a conserved architectural feature of LMTK3 and is appropriately represented by this broad term. Human topology is predicted and the UniProt location statement is transferred from mouse Q5XJV6, so the evidence is not a direct human membrane-localization assay. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB-SubCell:SL-0162 · UniProtKB membrane vocabulary term SUPPORTS TRANSFER The vocabulary mapping is accurate and agrees with the target's predicted transmembrane segment and the experimentally studied mouse ortholog. |
| GO:0030424 axon | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Axonal localization is an automatic mapping of a human UniProt statement transferred from mouse Lmtk3. It is plausible in the protein's brain-enriched neuronal context but has not been demonstrated for human Q96Q04. Reason: Retain as an orthology-supported, neuronal-context location rather than a core human localization. The source is direct for mouse Lmtk3 but indirect for the reviewed human protein. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB-SubCell:SL-0279 · UniProtKB axon vocabulary term SUPPORTS TRANSFER The mapping accurately reflects the current UniProt statement, whose underlying evidence is experimental mouse Lmtk3 localization. |
| GO:0030425 dendrite | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Dendritic localization is transferred from mouse Lmtk3 and is reinforced by later mouse hippocampal-neuron imaging, but it remains indirect for human Q96Q04. Reason: Retain as a biologically coherent neuronal-context location. It should not be promoted to a direct or core human localization because the available cellular evidence is from the mouse ortholog. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB-SubCell:SL-0283 · UniProtKB dendrite vocabulary term SUPPORTS TRANSFER The mapping reflects the current UniProt statement and is independently consistent with experimental dendritic localization of mouse Lmtk3. Supporting Evidence: PMID:38715938 Both LMTK3 and KCC2 were distributed evenly and along the dendritic processes, and the fluorescent signal overlapped with 31 ± 2 colocalized puncta found per 100 μm of dendritic length (Figure 2B). |
| GO:0106310 protein serine kinase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Correct specific catalytic activity. The Rhea mapping is corroborated by direct human LMTK3 assays on HSPB1 and RAB7A, while RCP Ser435 is a strong cellular LMTK3-dependent site. Reason: Protein serine kinase activity is experimentally established and is more informative than the generic protein kinase rows. The electronic Rhea assignment adds no biological overreach. Propagation Review Root cause: NO FAILURE CORE Sources checked: RHEA:17989 · L-seryl-protein phosphorylation reaction SUPPORTS TRANSFER The mapped reaction matches direct phosphorylation of serine substrates. Supporting Evidence: PMID:28294115 Phosphorylation of RCP at Ser435 by Lemur tyrosine kinase-3 (LMTK3) and of EphA2 at Ser897 by Akt are both necessary to promote Rab14-dependent (and Rab11-independent) trafficking of EphA2 which generates cell:cell repulsion events that drive tumour cells apart. PMID:40405280 Our results demonstrated that LMTK3 directly phosphorylates Rab7 in vitro and that this effect is abolished following LMTK3 pharmacological inhibition (Fig. 2j and Figure S2). |
| GO:0005515 protein binding | IPI PMID:21602804 Kinome screening for regulators of the estrogen receptor ide... | MODIFY | Summary: This IntAct row records physical interaction with ESR1/ERα (P03372), a nuclear estrogen receptor and reported LMTK3 phosphorylation substrate. The generic protein-binding term obscures the biologically relevant partner class. Reason: Replace uninformative protein binding with GO:0030331 nuclear estrogen receptor binding. The source row identifies ESR1 as the interacting partner, and the cited study reports LMTK3-dependent ERα phosphorylation and stabilization. Proposed replacements: nuclear estrogen receptor binding Supporting Evidence: PMID:21602804 LMTK3 phosphorylated ERα, protecting it from proteasomal degradation in vitro. |
| GO:0106310 protein serine kinase activity | EXP PMID:21602804 Kinome screening for regulators of the estrogen receptor ide... | ACCEPT | Summary: Direct experimental annotation of LMTK3's core catalytic activity. Although the cached source is abstract-only, it explicitly reports in-vitro ERα phosphorylation, and later full-text studies directly demonstrate serine-substrate phosphorylation by human LMTK3. Reason: Accept with curator deference to the full experimental paper and strong independent biochemical corroboration. RCP Ser435 and serine/threonine peptide substrates establish that LMTK3 is not merely a kinase-domain prediction. Supporting Evidence: PMID:21602804 LMTK3 phosphorylated ERα, protecting it from proteasomal degradation in vitro. PMID:28294115 Phosphorylation of RCP at Ser435 by Lemur tyrosine kinase-3 (LMTK3) and of EphA2 at Ser897 by Akt are both necessary to promote Rab14-dependent (and Rab11-independent) trafficking of EphA2 which generates cell:cell repulsion events that drive tumour cells apart. |
| GO:0005770 late endosome | IDA PMID:40405280 LMTK3 regulation of EV biogenesis and cargo sorting promotes... | NEW | Summary: Confocal imaging in human T47D and MDA-MB-231 cells places LMTK3 with RAB7A-positive late endosomes. Reason: Add the directly imaged late-endosome location. The microscopy establishes the RAB7A-positive compartment but does not by itself resolve the limiting membrane, so this conservative term is preferable to late endosome membrane. Supporting Evidence: PMID:40405280 Following immunofluorescence staining, our analysis showed overlapping localisation between LMTK3 and Rab7, confirming that LMTK3 is present in late endosomes |
| GO:1905750 negative regulation of endosome to plasma membrane protein transport | IMP PMID:28294115 Phosphorylation of Rab-coupling protein by LMTK3 controls Ra... | NEW | Summary: In human cancer cells, LMTK3 depletion or substitution of RAB11FIP1/RCP Ser435 blocks diversion of EPHA2 into a slower RAB14-dependent perinuclear route. Reason: Add the direction-specific transport annotation. Genetic perturbation, phosphosite detection, and phosphosite-mutant experiments show that LMTK3 and RAB11FIP1 Ser435 reduce EPHA2 return from endosomes to the plasma membrane; the extension records EPHA2 as the tested cargo. Purified LMTK3-RAB11FIP1 catalysis was not demonstrated. Supporting Evidence: PMID:28294115 HGF signalling achieves this by concomitant activation of two parallel phosphorylation cascades. HGF activates Akt to phosphorylate EphA2 on Ser897 and, in parallel with this, HGF signalling promotes LMTK3-mediated phosphorylation of RCP on Ser435 to favour RCP/Rab14 association and both of these events are necessary to divert EphA2 through a slower recycling pathway and promote cytoskeletal responses which enable cells to move apart. |
| GO:1902823 negative regulation of late endosome to lysosome transport | IMP PMID:40405280 LMTK3 regulation of EV biogenesis and cargo sorting promotes... | NEW | Summary: LMTK3-dependent RAB7A Ser72 phosphorylation reduces endocytic-cargo degradation and disrupts late-endosome trafficking in human breast-cancer cells. Reason: Add the direction-specific process annotation supported by LMTK3 perturbation, RAB7A Ser72 mutants, reduced EGFR degradation, and enlarged multivesicular bodies. This term captures impaired late-endosome-to-lysosome transport without asserting an increase in extracellular-vesicle number. Supporting Evidence: PMID:40405280 Mechanistically, we provide evidence that LMTK3 phosphorylates Rab7, a key regulator of multivesicular body (MVB) trafficking, thereby reducing the fusion of MVBs with lysosomes and subsequent degradation of intralumenal vesicles, resulting in altered EV release. |
| GO:0008157 protein phosphatase 1 binding | IPI PMID:26212333 LMTK3 Represses Tumor Suppressor-like Genes through Chromati... | NEW | Summary: Human LMTK3 participates with PPP1CA/PP1alpha in a nuclear LMTK3-TRIM28/KAP1-PP1alpha scaffolding mechanism in breast-cancer cells, and cached full-text evidence independently states that the LMTK3 C-terminus binds PP1. Reason: Add the specific PP1-binding activity. The cached human abstract supports a PP1alpha-dependent nuclear scaffold, while cached full-text PMID:38715938 explicitly states that the large disordered LMTK3 cytoplasmic C-terminus binds PP1. Together these sources support a binding/scaffolding function, not phosphatase activity by LMTK3; assay- and motif-level details unavailable in the local human-paper cache are not asserted here. Supporting Evidence: PMID:26212333 The LMTK3/KAP1 interaction is stabilized by PP1α, which suppresses KAP1 phosphorylation specifically at LMTK3-associated chromatin regions, inducing chromatin condensation and resulting in transcriptional repression of LMTK3-bound tumor suppressor-like genes. PMID:38715938 LMTK3 consists of 1,460 amino acids with a small extracellular N-terminus, a single transmembrane domain, an adjacent catalytic domain, and large highly disordered cytoplasmic C-terminus that binds PP1 |
| GO:0033148 positive regulation of intracellular estrogen receptor signaling pathway | IMP PMID:21602804 Kinome screening for regulators of the estrogen receptor ide... | NEW | Summary: LMTK3 promotes ESR1/ERalpha stability and abundance in estrogen-receptor-positive human breast-cancer models. Reason: Add the missing positive-regulation process annotation. Direct in-vitro ESR1 phosphorylation and loss-of-function phenotypes support the direction, but this is a disease- and cell-context role rather than a universal core function; the ESR1 phosphosite remains unknown. Supporting Evidence: PMID:21602804 LMTK3 phosphorylated ERα, protecting it from proteasomal degradation in vitro. |
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Download this section (compressed HTML)Q: Does purified current-sequence human LMTK3 phosphorylate tyrosine as well as serine and threonine substrates?
Q: What ESR1 and CDC37 residues are directly phosphorylated by LMTK3, and is RAB11FIP1 Ser435 a purified-enzyme substrate or a cellularly indirect site?
Q: Where does endogenous LMTK3 localize and orient in non-transformed human cells and human neurons?
Q: Is PP1 targeting a kinase-independent, conserved LMTK3 activity in both the human TRIM28/KAP1 and neuronal SLC12A5/KCC2 modules?
Q: Do translated human LMTK3 products exist beyond the current unnumbered 1460-residue UniProt product?
Q: Are RAB7A-dependent changes in multivesicular bodies and extracellular vesicles physiological outside LMTK3-overexpressing breast-cancer models?
Experiment: Test purified current Q96Q04 kinase on matched serine, threonine, and tyrosine phosphoacceptor libraries with current-coordinate kinase-dead controls, phospho-amino-acid analysis, and an active-state structural determination.
Experiment: Map ESR1 and CDC37 phosphosites and test RAB11FIP1 Ser435 using purified proteins, endogenous LMTK3 knockout, wild-type versus catalytic-dead rescue, and phosphosite-mutant functional rescue.
Experiment: Determine endogenous LMTK3 topology and Golgi, late-endosome, recycling-endosome, axonal, dendritic, and nuclear localization in non-transformed human cells and iPSC-derived neurons using validated Q96Q04 reagents.
Experiment: Mutate the current Q96Q04 PP1-docking motif and compare wild-type and kinase-dead rescue for PPP1CA binding, TRIM28/KAP1 dephosphorylation and chromatin repression, and SLC12A5/KCC2 dephosphorylation and chloride extrusion in human neurons.
Experiment: Use long-read RNA sequencing, protein N-terminomics, and targeted proteomics to determine whether alternative human LMTK3 protein products exist, mapping every construct and residue to the current 1460-residue Q96Q04 sequence.
Experiment: Compare endogenous genetic perturbation with acute catalytic inhibition across normal and breast-cancer cell models while measuring RAB7A Ser72 phosphorylation, endosome-to-lysosome flux, and extracellular-vesicle number, size, and cargo; include controls that separate C28-mediated catalytic inhibition from LMTK3 destabilization.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: Whether current-sequence human LMTK3 has intrinsic protein tyrosine kinase activity remains unresolved.
OPEN BIOLOGY MF_DARK
What is known: Direct assays establish serine phosphorylation, whereas the historical "lemur tyrosine kinase" name, an active-site signature, and predicted dual specificity do not establish a tyrosine phosphoacceptor reaction.
Significance: Resolving phosphoacceptor specificity is necessary to define the enzyme without perpetuating a historical naming inference.
What would resolve it: Compare purified current Q96Q04 kinase activity on matched serine, threonine, and tyrosine substrates with kinase-dead controls and phospho-amino-acid analysis.
Gap: Directness and site resolution remain incomplete for several proposed human LMTK3 substrates.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: RAB7A Ser72 and HSPB1 Ser15/Ser82 are purified-enzyme-supported sites; CDC37 is phosphorylated directly at an unmapped site, ESR1 is phosphorylated in vitro at an unmapped site, and RAB11FIP1 Ser435 is strongly LMTK3-dependent in cells but lacks a purified-enzyme assay.
Significance: Direct substrate maps are needed to connect LMTK3 catalysis to its distinct cellular pathways and to separate direct targets from indirect phosphoproteomic changes.
What would resolve it: Use endogenous LMTK3 knockout and catalytic-dead rescue, purified current-sequence kinase assays, phosphosite mapping, and phosphosite-mutant rescue for each candidate.
Gap: Endogenous human LMTK3 topology and localization outside cancer-cell models are incompletely established.
OPEN BIOLOGYCURATION RESIDUAL_SUBGAP
What is known: Current human membrane, Golgi, axon, and dendrite statements are transferred from mouse Q5XJV6; direct human imaging places LMTK3 at RAB7A-positive late endosomes in two breast-cancer cell lines.
Significance: Direct localization is needed to determine where the kinase and PP1-scaffold modules operate physiologically in human cells.
What would resolve it: Use validated endogenous Q96Q04 reagents, protease-protection topology assays, and quantitative colocalization in non-transformed human cells and iPSC-derived neurons.
Gap: The breadth and kinase dependence of LMTK3's PP1-targeting scaffold function remain unresolved.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Human breast-cancer cells support a PPP1CA-TRIM28/KAP1 chromatin module, whereas the PP1-SLC12A5/KCC2 mechanism and neuronal physiology are established mainly in mouse tissue and neurons.
Significance: This determines whether PP1 targeting is a conserved, catalytic-independent core activity or a collection of tissue-specific interactions.
What would resolve it: Mutate the current-sequence PP1-docking motif, compare wild-type and kinase-dead rescue, and assay endogenous chromatin and KCC2 modules in human cells and neurons.
Gap: Biologically relevant alternative human LMTK3 protein products have not been established.
OPEN BIOLOGYCURATION RESIDUAL_SUBGAP
What is known: The reviewed 1460-residue Q96Q04 record has no curated ALTERNATIVE PRODUCTS section; transcript cross-references and older 1489-residue experimental constructs do not justify numbered protein isoforms or unconverted residue coordinates.
Significance: Product-level resolution is required before assigning isoform-specific topology, localization, or function and before reusing historical residue numbers.
What would resolve it: Combine long-read transcript sequencing, protein N-terminomics, and targeted proteomics, and report all constructs against the current Q96Q04 sequence.
Gap: The physiological scope of the RAB7A-dependent multivesicular-body and extracellular-vesicle phenotype is unknown.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Current direct evidence comes from LMTK3 overexpression and perturbation in human breast-cancer cells and supports altered vesicle size, subpopulation, and cargo, not a general increase in extracellular-vesicle number.
Significance: This distinguishes a general endosomal function from an overexpression- or cancer-specific consequence.
What would resolve it: Quantify endogenous RAB7A Ser72 phosphorylation, endosome-to-lysosome flux, and vesicle number, size, and cargo after genetic LMTK3 perturbation across normal and disease-relevant human cell types.
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