Affinage

RNF167

E3 ubiquitin-protein ligase RNF167 · UniProt Q9H6Y7

Length
350 aa
Mass
38.3 kDa
Annotated
2026-04-28
10 papers in source corpus 11 papers cited in narrative 11 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RNF167 is a transmembrane RING-type E3 ubiquitin ligase that resides on endosomes and lysosomes—dependent on its protease-associated (PA) domain—and ubiquitinates diverse substrates using atypical ubiquitin chain linkages to regulate endolysosomal trafficking, mTORC1 nutrient sensing, synaptic plasticity, and innate immune signaling. It ubiquitinates AMPA receptor subunits via a two-step mechanism in which UBE2D1 primes monoubiquitination and UBE2N extends K63-linked chains, reducing synaptic AMPAR surface expression (PMID:23129617, PMID:33650289). RNF167 targets the lysosome-positioning GTPase Arl8B (K141) and GTP-bound Rab7 for ubiquitin-dependent degradation, controlling lysosome distribution and endocytic flux (PMID:27808481, PMID:35887194), and regulates mTORC1 through opposing ubiquitination events on CASTOR1 (K29-linked chains promoting proteasomal degradation to activate mTORC1) and Sestrin2 (polyubiquitination enhancing GATOR2 binding to inhibit mTORC1) (PMID:33594058, PMID:35114100). It also attaches K6-linked chains to the CARD domains and K11-linked chains to the CTD domains of RIG-I and MDA5, directing them to autophagic and proteasomal degradation respectively, thereby suppressing type I interferon signaling (PMID:39994288).

Mechanistic history

Synthesis pass · year-by-year structured walk · 7 steps
  1. 2012 High

    Establishing RNF167 as a lysosomal E3 ligase that controls synaptic AMPAR levels answered the question of whether endolysosomal ubiquitin ligases directly regulate ionotropic receptor trafficking at synapses.

    Evidence shRNA knockdown, RING-dead mutant, surface expression assays, and electrophysiology in hippocampal neurons

    PMID:23129617

    Open questions at the time
    • Ubiquitination sites on AMPAR subunits not mapped
    • E2 conjugating enzymes not identified
    • Mechanism linking lysosomal RNF167 to surface receptor removal unclear
  2. 2014 High

    Demonstrating that the PA domain controls endosomal targeting while the RING domain provides catalytic activity resolved how RNF167 couples its enzymatic function to correct subcellular localization, and showed that cancer-associated PA mutations cause mislocalization without loss of ligase activity.

    Evidence Systematic mutagenesis of RING and PA domains with in vitro ubiquitination assays and subcellular localization microscopy

    PMID:24387786

    Open questions at the time
    • Structural basis of PA domain–membrane interaction unknown
    • Whether PA-mutant mislocalization contributes to tumorigenesis not tested in vivo
  3. 2016 High

    Identifying Arl8B as a direct RNF167 substrate ubiquitinated at K141 established a mechanism by which RNF167 controls lysosome positioning and endocytic trafficking to lysosomes.

    Evidence BioID proximity labeling for substrate discovery, in vitro ubiquitination, K141R mutagenesis, lysosome positioning and trafficking assays

    PMID:27808481

    Open questions at the time
    • Ubiquitin chain type on Arl8B not determined
    • Whether Arl8B degradation is proteasomal or lysosomal not resolved
  4. 2021 High

    Two studies revealed the E2 selectivity of RNF167 (UBE2D1 primes, UBE2N extends K63 chains on GluA2) and identified CASTOR1 as a substrate whose K29-linked ubiquitination by RNF167 integrates AKT phosphorylation with mTORC1 activation, answering how RNF167 builds specific ubiquitin chain types and connects to nutrient signaling.

    Evidence In vitro reconstitution of E2–E3 ubiquitination cascade with kinetic analysis and pharmacological UBE2N inhibition in neurons; Co-IP, ubiquitin linkage analysis, phosphorylation assays, and xenograft models for CASTOR1

    PMID:33594058 PMID:33650289

    Open questions at the time
    • Whether UBE2D1/UBE2N pairing applies to non-AMPAR substrates unknown
    • Structural basis of RNF167–CASTOR1 recognition not determined
  5. 2022 High

    Discovery that RNF167 ubiquitinates Sestrin2 to promote GATOR2 interaction and suppress mTORC1 in response to leucine, and ubiquitinates GTP-bound Rab7 affecting late endosome morphology, broadened RNF167's role to nutrient-responsive mTORC1 inhibition and endosomal GTPase regulation.

    Evidence CRISPR knockout, cell-permeable peptide, xenograft models for Sestrin2; in vitro ubiquitination, subcellular fractionation, vesicle size analysis for Rab7

    PMID:35114100 PMID:35887194

    Open questions at the time
    • Ubiquitin chain type on Rab7 not determined
    • Ubiquitination sites on Rab7 not mapped
    • How RNF167 exerts opposing effects on mTORC1 via CASTOR1 versus Sestrin2 is not integrated
  6. 2023 Medium

    Identification of Tollip as a substrate receiving K33-linked ubiquitin at K235, required for Tollip-mediated suppression of TNF-α-induced NF-κB and JNK signaling, expanded RNF167's repertoire to inflammatory signaling regulation via atypical chain types.

    Evidence Reciprocal Co-IP, ubiquitin linkage analysis, K235R mutagenesis, NF-κB/MAPK reporter assays

    PMID:37410058

    Open questions at the time
    • Single-lab finding awaiting independent replication
    • Whether RNF167–Tollip axis operates in vivo during inflammation not tested
    • Mechanism of K33 chain recognition by downstream effectors unknown
  7. 2025 High

    Mechanistic dissection of dual ubiquitin chain types on RIG-I/MDA5 (K6-linked on CARD for autophagic degradation via p62; K11-linked on CTD for proteasomal degradation) revealed how RNF167 suppresses antiviral innate immunity through two synergistic degradation pathways.

    Evidence Domain-specific mutagenesis, linkage-specific ubiquitin analysis, autophagy flux assays, proteasome inhibitor experiments, IFN-I reporters, RNF167 knockout

    PMID:39994288

    Open questions at the time
    • In vivo relevance during viral infection not demonstrated
    • How RNF167 selects K6 versus K11 linkages on different domains mechanistically unclear
    • E2 enzymes mediating K6 and K11 chain assembly not identified

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include how RNF167 coordinates opposing effects on mTORC1 (CASTOR1 degradation activates, Sestrin2 ubiquitination inhibits), the structural basis of PA domain-mediated membrane targeting, and whether the RNF167–RNF13 heterodimer represents a physiologically relevant complex with distinct substrate specificity.
  • No structural model of full-length RNF167 or its PA domain–membrane interaction
  • Context-dependent regulation of RNF167 toward opposing mTORC1 outcomes not resolved
  • RNF167–RNF13 heterodimer function supported only by preprint data

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 9
Localization
GO:0005764 lysosome 3 GO:0005768 endosome 2
Pathway
R-HSA-392499 Metabolism of proteins 8 R-HSA-162582 Signal Transduction 3 R-HSA-112316 Neuronal System 2 R-HSA-5653656 Vesicle-mediated transport 2 GO:0005886 plasma membrane 1 R-HSA-168256 Immune System 1 R-HSA-9612973 Autophagy 1
Partners
ARL8BCASTOR1DDX58RAB7ASESN2TOLLIPUBE2D1UBE2N

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2012 RNF167 is a transmembrane RING domain-containing E3 ubiquitin ligase that is predominantly lysosomal (with a subpopulation on the neuronal surface) and ubiquitinates AMPA receptor subunits in an activity-dependent manner, thereby reducing AMPAR surface expression and synaptic AMPAR currents without affecting NMDAR currents. shRNA knockdown, RING-dead mutant overexpression, surface expression assays, electrophysiology in hippocampal neurons, subcellular localization by fluorescence microscopy Proceedings of the National Academy of Sciences of the United States of America High 23129617
2014 Point mutations in the RING domain of RNF167 abrogate its E3 ubiquitin ligase activity, and the PA (protease-associated) domain is required for endosomal localization; PA domain mutations found in human tumors retain ligase activity but cause mislocalization, indicating both enzymatic activity and correct localization are needed for substrate targeting. Mutagenesis of RING and PA domains, ubiquitination assays, subcellular localization microscopy The Biochemical journal High 24387786
2016 RNF167 ubiquitinates the small GTPase Arl8B at lysine K141, targeting it for degradation; RNF167 overexpression reduces Arl8B levels and alters lysosome positioning and endocytic trafficking to lysosomes, effects that are counteracted by the ubiquitination-defective Arl8B K141R mutant. Proximity-dependent biotin labeling (BioID) for substrate identification, in vitro ubiquitination assay, site-directed mutagenesis (K141R), overexpression/knockdown with lysosome positioning and endocytic trafficking readouts The FEBS journal High 27808481
2021 RNF167 ubiquitinates CASTOR1 with K29-linked polyubiquitin chains, leading to its proteasomal degradation; AKT phosphorylates CASTOR1 at S14, which increases CASTOR1 binding to RNF167 and promotes its ubiquitination/degradation while reducing its binding to MIOS, thereby activating mTORC1 in an arginine-independent manner. Co-immunoprecipitation, in vitro ubiquitination assays, ubiquitin linkage-specific analysis, phosphorylation assays, mTORC1 activity readouts, knockdown/knockout with xenograft tumor models Nature communications High 33594058
2021 RNF167 functionally interacts with E2 conjugating enzymes UBE2D1 and UBE2N; UBE2N drives K63-linked polyubiquitination of GluA2 (AMPAR subunit) only after GluA2 has been primed by a UBE2D1-initiated monoubiquitin, and pharmacological inhibition of UBE2N in hippocampal neurons reduces AMPA-induced GluA2 ubiquitination. In vitro autoubiquitination assays, binding assays with kinetic analysis, fluorescence microscopy co-localization, computational modeling of RING–E2 interaction, pharmacological inhibition of UBE2N in primary neurons The FEBS journal High 33650289
2022 RNF167 (E3) and deubiquitinase STAMBPL1 oppositely control polyubiquitination of Sestrin2; RNF167-mediated ubiquitination of Sestrin2 promotes its interaction with GATOR2 and inhibits mTORC1 signaling in response to leucine availability. Co-immunoprecipitation, ubiquitination assays, mTORC1 activity measurements, CRISPR knockout and heterozygous mutation correction, cell-permeable peptide blocking STAMBPL1-Sestrin2 interaction, xenograft tumor models Molecular cell High 35114100
2022 RNF167 ubiquitinates Rab7 in a manner dependent on Rab7 being in its GTP-bound active (membrane-anchored) form; RNF167-mediated ubiquitination affects Rab7 membrane localization and results in larger Rab7-positive vesicles, and Charcot-Marie-Tooth Type 2B disease variants of Rab7 impair RNF167-mediated ubiquitination. Immunoprecipitation, in vitro ubiquitination assays, subcellular fractionation, epifluorescence microscopy, RNF167 knockdown with Lamp1 and vesicle size readouts International journal of molecular sciences Medium 35887194
2023 RNF167 interacts with Tollip via Tollip's CUE domain and attaches K33-linked polyubiquitin chains to Tollip at K235; this ubiquitination is required for Tollip to suppress TNF-α-induced NF-κB and MAPK (JNK) signaling, as the K235R Tollip mutant fails to inhibit these cascades. Co-immunoprecipitation, in vitro/cellular ubiquitination assays, ubiquitin linkage analysis, K235R point mutagenesis, NF-κB/MAPK reporter/kinase assays FASEB journal Medium 37410058
2025 RNF167 attaches atypical K6-linked polyubiquitin chains to the CARD domains of RIG-I and MDA5, marking them for p62-mediated selective autophagic degradation in autolysosomes; it also attaches K11-linked polyubiquitin chains to the CTD domains of RIG-I/MDA5, targeting them for proteasomal degradation. Both pathways synergistically suppress RLR-triggered type I interferon signaling. Co-immunoprecipitation, in vitro ubiquitination assays, ubiquitin linkage-specific analysis, domain-specific mutagenesis, autophagy flux assays (p62 interaction), proteasome inhibitor experiments, IFN-I reporter assays, RNF167 knockout Nature communications High 39994288
2025 RNF167 forms a heterodimer with the related E3 ubiquitin ligase RNF13, and this heterodimer modifies both RNF13 and RNF167 lysosomal trafficking; the heterodimer interacts with and alters IDS (iduronate 2-sulfatase) glycosylation and maturation differently than either protein alone, though RNF167's catalytic activity is not required for generating the underglycosylated IDS form. Co-immunoprecipitation, AlphaFold3 structural prediction (functional co-IP validation), catalytic mutant analysis, glycosylation and lysosomal trafficking assays bioRxiv (preprint)preprint Low bio_10.1101_2025.06.20.660705
2025 SMAD3 stabilizes Sestrin2 protein by modulating the balance between RNF167-mediated ubiquitination and STAMBPL1-mediated deubiquitination of Sestrin2, as shown by co-immunoprecipitation of SMAD3 with both enzymes. Co-immunoprecipitation, Western blotting, RT-qPCR, immunofluorescence, SMAD3 overexpression/knockdown Cell division Low 40751214

Source papers

Stage 0 corpus · 10 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2022 E3 ligase RNF167 and deubiquitinase STAMBPL1 modulate mTOR and cancer progression. Molecular cell 71 35114100
2012 Ubiquitin ligase RNF167 regulates AMPA receptor-mediated synaptic transmission. Proceedings of the National Academy of Sciences of the United States of America 69 23129617
2021 RNF167 activates mTORC1 and promotes tumorigenesis by targeting CASTOR1 for ubiquitination and degradation. Nature communications 41 33594058
2014 Tumour-associated mutations of PA-TM-RING ubiquitin ligases RNF167/RNF13 identify the PA domain as a determinant for endosomal localization. The Biochemical journal 30 24387786
2016 RNF167 targets Arl8B for degradation to regulate lysosome positioning and endocytic trafficking. The FEBS journal 24 27808481
2021 Functional interaction of ubiquitin ligase RNF167 with UBE2D1 and UBE2N promotes ubiquitination of AMPA receptor. The FEBS journal 12 33650289
2023 RNF167-mediated ubiquitination of Tollip inhibits TNF-α-triggered NF-κB and MAPK activation. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 10 37410058
2022 Membrane Targeting and GTPase Activity of Rab7 Are Required for Its Ubiquitination by RNF167. International journal of molecular sciences 6 35887194
2025 RNF167 mediates atypical ubiquitylation and degradation of RLRs via two distinct proteolytic pathways. Nature communications 3 39994288
2025 SMAD3 orchestrates RNF167 and STAMBPL1-mediated Sestrin2 ubiquitination to drive gastric cancer progression. Cell division 0 40751214