LNX2 is a multidomain RING-type E3 ubiquitin ligase. Its N-terminal Zn-RING-Zn module cooperates with UbcH5-family E2 enzymes, while an NPXY motif and four C-terminal PDZ domains organize substrate and partner recognition. Full-length human LNX2 autoubiquitinates and directly polyubiquitinates NUMB in vitro. In cellular and model-organism contexts, its scaffold/ligase architecture also regulates selected membrane proteins and trafficking pathways, including CD8α, GlyT2, and connexin36. These downstream roles are substrate- and cell-type-dependent; LNX2 is not known to belong to one stable obligate complex.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004842 ubiquitin-protein transferase activity | IBA GO_REF:0000033 | MODIFY | Summary: The phylogenetic annotation captures LNX2's RING E3 activity, but the parent transferase term is less specific than the experimentally established ubiquitin protein ligase activity. Reason: Direct assays with full-length human LNX2 show UbcH5-dependent autoubiquitination and polyubiquitination of human NUMB. GO:0061630 names this E3-specific activity more precisely than GO:0004842 while retaining the valid biological essence of the IBA. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002717501 · PANTHER ancestral node SUPPORTS TRANSFER The phylogenetic node supports conservation of RING E3 ligase activity. ZFIN:ZDB-GENE-060228-2 · zebrafish lnx2b SUPPORTS TRANSFER A vertebrate LNX2-family source supporting transfer to human LNX2. Proposed replacements: ubiquitin protein ligase activity Supporting Evidence: PMID:26451611 We expressed the full-length LNX2 (FL-LNX2) and identified that the UbcH5 E2 family is involved in mediating the E3 ligase activity of LNX2 using the E2 profiling kit (Life Sensors) (Figure 1A). |
| GO:0005515 protein binding | IPI PMID:21516116 Next-generation sequencing to generate interactome datasets. | MARK AS OVER ANNOTATED | Summary: A high-throughput human interactome screen detected interactions involving LNX2. Reason: PMID:21516116 reports a systematic interaction-mapping dataset, and the listed partners support physical interactions. However, GO:0005515 is an uninformative generic binding term that does not identify LNX2's PDZ-mediated recognition or RING E3 ligase function. The interactions should be retained in an interaction database, but this GO molecular-function annotation is over-annotated. |
| GO:0005515 protein binding | IPI PMID:22458338 Host-pathogen interactome mapping for HTLV-1 and -2 retrovir... | MARK AS OVER ANNOTATED | Summary: LNX2 was detected as a host interactor of HTLV proteins in a systematic screen. Reason: PMID:22458338 supports physical host-pathogen interactions through systematic yeast two-hybrid screening and retesting. Nevertheless, generic protein binding does not describe a biologically informative molecular function of LNX2 or establish that these viral interactions are part of its normal cellular role, so the GO annotation is over-annotated. |
| GO:0005515 protein binding | IPI PMID:23088713 Protein interactions of the transcription factor Hoxa1. | MARK AS OVER ANNOTATED | Summary: A systematic HOXA1 interactome study detected an LNX2-HOXA1 interaction. Reason: PMID:23088713 reports yeast two-hybrid screening with orthogonal interaction assays, so the physical interaction is plausible even though the cached record is abstract-only. GO:0005515 remains too generic to express LNX2's molecular function and the screen does not establish a core functional role for the interaction. |
| GO:0005515 protein binding | IPI PMID:27107012 Pooled-matrix protein interaction screens using Barcode Fusi... | MARK AS OVER ANNOTATED | Summary: Barcode-fusion interaction screening detected LNX2 interactions with two proteins. Reason: PMID:27107012 is a high-throughput protein-interaction methods study and supports the listed experimental interaction calls. The generic term protein binding adds no mechanistic information about LNX2's PDZ scaffold or RING E3 activity, and isolated screening interactions should not be treated as a core GO molecular function. |
| GO:0005515 protein binding | IPI PMID:29892012 An interactome perturbation framework prioritizes damaging m... | MARK AS OVER ANNOTATED | Summary: A large interaction-perturbation study included multiple LNX2 interaction pairs. Reason: PMID:29892012 experimentally assays protein interactions in a broad disease-variant framework, supporting the listed interaction observations. GO:0005515 is nevertheless non-specific and does not capture the interaction domain, substrate relationship, or ubiquitin-transfer mechanism, so it is not an informative LNX2 function annotation. |
| GO:0005515 protein binding | IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari... | MARK AS OVER ANNOTATED | Summary: A population-variant interaction study assayed multiple LNX2 interaction pairs. Reason: PMID:31515488 supports experimental interaction measurements in a systematic variant screen. The evidence is suitable for recording individual interactions, but the catch-all molecular-function term protein binding is not informative about LNX2's conserved activity and therefore represents GO over-annotation. |
| GO:0005515 protein binding | IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... | MARK AS OVER ANNOTATED | Summary: A neurodegenerative-disease interactome map detected LNX2 with multiple partners. Reason: PMID:32814053 supports a large-scale set of protein interaction observations, but the cached publication is abstract-only and does not establish a normal, core LNX2 role for each pair. Generic protein binding is also too broad to convey LNX2's PDZ-mediated recognition or RING E3 activity, so this GO annotation is over-annotated. |
| GO:0005515 protein binding | IPI PMID:33864728 Host PDZ-containing proteins targeted by SARS-CoV-2. | MARK AS OVER ANNOTATED | Summary: LNX2 PDZ domains bind SARS-CoV and SARS-CoV-2 proteins in affinity profiling. Reason: PMID:33864728 directly identifies LNX2 among human PDZ proteins bound by coronavirus proteins, with measured micromolar affinities. That supports the interactions, but GO:0005515 discards the informative PDZ-dependent context and describes a pathogen interaction rather than a demonstrated core cellular function of LNX2. |
| GO:0005515 protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | MARK AS OVER ANNOTATED | Summary: Quantitative fragmentomics mapped a very large set of LNX2 interaction candidates. Reason: PMID:36115835 is a proteome-scale affinity-mapping study, and the extensive supporting entity list records its interaction calls. These data are appropriate as interaction evidence but do not make generic protein binding a useful GO molecular function; many fragment-level or context-free contacts cannot be equated with LNX2's core role. |
| GO:0042802 identical protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | KEEP AS NON CORE | Summary: Proteome-scale interactome mapping detected LNX2 self-association. Reason: The IPI annotation from PMID:25416956 directly records an LNX2-LNX2 interaction, so identical protein binding is a reasonable description of the observed self-association. Because the result comes from a large-scale binary interaction map and no obligate LNX2 homomeric complex or catalytic requirement is established, it is retained as a non-core property rather than a defining function. |
| GO:0042802 identical protein binding | IPI PMID:36115835 Quantitative fragmentomics allow affinity mapping of interac... | KEEP AS NON CORE | Summary: Quantitative fragmentomics detected self-association of LNX2. Reason: PMID:36115835 provides direct interaction evidence consistent with LNX2 identical protein binding. Self-association is plausible for a multidomain PDZ scaffold, but the proteome-scale affinity assay does not show that homomerization is required for LNX2's ubiquitin-ligase activity, so this is retained as non-core. |
| GO:0005886 plasma membrane | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Plasma-membrane localization is inferred from the mouse Lnx2 orthologue. Reason: The orthology transfer in GO_REF:0000107 uses the reviewed mouse Lnx2 protein and its matching Ensembl identifier. Plasma-membrane association is compatible with a PDZ scaffold that engages membrane-associated partners, but localization can be cell-type and interaction dependent and is not the defining activity of LNX2. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:Q91XL2 · mouse Lnx2 protein SUPPORTS TRANSFER The mammalian orthologue supports transfer of the localization. ensembl:ENSMUSP00000016664 · mouse Lnx2 Ensembl protein CIRCULAR OR REDUNDANT A second identifier for the same mouse source protein, not independent evidence. |
| GO:0030165 PDZ domain binding | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: PDZ domain binding is inferred from the mouse Lnx2 orthologue. Reason: The transfer in GO_REF:0000107 comes from the mammalian Lnx2 orthologue. This activity is compatible with LNX2's multidomain interaction architecture and with the reported oligomerization of Lnx proteins through PDZ-domain interactions. It is more informative than generic protein binding, but remains a secondary interaction property rather than the defining RING E3 activity of LNX2. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:Q91XL2 · mouse Lnx2 protein SUPPORTS TRANSFER The direct mammalian orthologue supports transfer of PDZ domain binding. ensembl:ENSMUSP00000016664 · mouse Lnx2 Ensembl protein CIRCULAR OR REDUNDANT A redundant identifier for the same mouse donor rather than a second source. Supporting Evidence: PMID:11922143 In addition, Lnx proteins form oligomers either via their PDZ domains binding to PDZ-binding consensus motifs located in their C-termini or by homophilic oligomerization of their RING fingers. |
| GO:0042802 identical protein binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Identical protein binding is inferred by an ARBA rule from mouse Lnx2. Reason: The rule-based inference is consistent with two independent human IPI annotations for LNX2 self-association (PMID:25416956 and PMID:36115835). Thus the transferred term is biologically defensible, but self-binding remains a secondary property because an obligate functional LNX2 homomer has not been demonstrated. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: ARBA:ARBA00027930 · ARBA identical-protein-binding rule SUPPORTS TRANSFER The automated rule yields a term independently corroborated by human IPI evidence. UniProtKB:Q91XL2 · mouse Lnx2 protein SUPPORTS TRANSFER The mammalian orthologue is an appropriate biological donor. ensembl:ENSMUSP00000016664 · mouse Lnx2 Ensembl protein CIRCULAR OR REDUNDANT A redundant identifier for the same mouse source protein. |
| GO:0000209 protein polyubiquitination | IDA PMID:26451611 Structural basis for the indispensable role of a unique zinc... | NEW | Summary: Full-length human LNX2 directly polyubiquitinates human NUMB in a reconstituted UbcH5b-dependent assay. Reason: Protein polyubiquitination is a direct output of the experimentally established RING E3 activity and is absent from the current human LNX2 GOA set. The has_input extension records NUMB as the assayed substrate without treating an IDA substrate as WITH/FROM evidence. Supporting Evidence: PMID:26451611 We observed that human Numb acts as a substrate for FL-LNX2 and undergoes polyubiquitination (Figure 2A and 2B). |
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Download this section (compressed HTML)Q: Which endogenous human proteins are direct physiological LNX2 substrates in each relevant cell type, and what substrate features are recognized by its NPXY- and PDZ-mediated interaction modules?
Q: What ubiquitin-chain architectures and downstream fates does LNX2 impose on each substrate in vivo, and when does autoubiquitination regulate those outputs?
Q: Does LNX2 self-association alter substrate selection, localization, or signaling even though Zn-RING-Zn dimerization is dispensable for autoubiquitination in vitro?
Experiment: Endogenously tag LNX2 in selected human neuronal, epithelial, and immune cell models; combine acute LNX2 degradation with diGly ubiquitin-remnant proteomics, quantitative proteomics, and proximity labeling. Validate candidate direct substrates by purified reconstitution and rescue with wild-type LNX2 versus RING-inactive, NPXY-mutant, and individual PDZ-domain mutants.
Hypothesis: LNX2 ubiquitinates a restricted, cell-type-specific substrate set that extends beyond NUMB and is selected through its NPXY motif and individual PDZ domains.
Type: endogenous perturbation and ubiquitin-remnant proteomics
Experiment: For validated endogenous substrates, map ubiquitin sites and chain linkages by targeted mass spectrometry after acute LNX2 perturbation, then measure substrate stability, trafficking, and endocytosis with proteasome and lysosome controls. Compare wild-type LNX2 with Zn-RING-Zn and interaction-module mutants.
Hypothesis: Substrate identity and interaction-module engagement determine the ubiquitin linkage and cellular fate produced by LNX2.
Type: linkage-resolved substrate fate analysis
Experiment: Introduce endogenous oligomerization-disrupting alleles and quantify LNX2 stoichiometry, localization, interactomes, and substrate ubiquitination while confirming preserved intrinsic E3 activity in purified assays.
Hypothesis: LNX2 oligomerization tunes substrate selection or localization without being required for catalytic ubiquitin transfer.
Type: endogenous structure-function analysis
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The physiological substrate hierarchy of human LNX2 is unresolved: NUMB is a direct substrate in a purified assay, but the dominant endogenous substrates and relevant cell types have not been established.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Full-length human LNX2 directly polyubiquitinates human NUMB in vitro, whereas Lnx1/Lnx2 double-knockout mouse brain retains normal NUMB abundance and lacks major neuroanatomical defects indicative of altered NUMB function.
Significance: Resolving this gap is necessary to distinguish a broadly relevant LNX2-NUMB axis from context-specific substrate relationships and to assign supported downstream biological processes.
What would resolve it: Acute endogenous LNX2 perturbation coupled to ubiquitin-remnant and abundance proteomics across relevant human cell types, followed by biochemical validation of direct candidates, would establish the physiological substrate hierarchy.
Provenance (the field's own admissions):
Gap: How the NPXY motif, four PDZ domains, and self-association cooperate with the Zn-RING-Zn catalytic module to select substrates and control LNX2 localization is not known at endogenous expression levels.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: LNX2 has experimentally supported scaffold interactions and self-association, but self-association is dispensable for Zn-RING-Zn autoubiquitination and no stable obligate LNX2 complex has been established.
Significance: This mechanism would explain how a conserved E3 catalytic module produces substrate- and cell-context-specific trafficking and signaling outputs.
What would resolve it: Endogenous domain-selective alleles combined with quantitative interactomics, localization measurements, and substrate-specific ubiquitination assays would separate recruitment, scaffolding, oligomerization, and catalytic roles.
Provenance (the field's own admissions):
Gap: The ubiquitin-chain architectures and downstream fates generated by LNX2 on physiological substrates in cells remain unresolved.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: Purified full-length LNX2 can form polyubiquitin through all seven lysine linkages and can polyubiquitinate NUMB, but these in-vitro results do not define linkage preference or substrate fate in cells.
Significance: Linkage and fate determine whether LNX2 primarily controls substrate degradation, trafficking, signaling, or a mixture of context-specific outcomes.
What would resolve it: Linkage-resolved ubiquitinomics and matched measurements of substrate stability and trafficking after acute endogenous LNX2 perturbation would resolve this gap.
Provenance (the field's own admissions):
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