UBXN6

UBXN6/UBXD1 is a multi-domain cofactor of the AAA+ ATPase p97/VCP that couples p97 to selective protein extraction and organelle quality-control pathways (PMID:21822278, PMID:27753622). It engages p97 through multiple interfaces: a PUB domain that binds the extreme C-terminus of p97 (an interaction abolished by phosphorylation of the penultimate tyrosine) (PMID:18656546, PMID:31847414), an intrinsically disordered N-terminal region that intercalates into the p97 N-domain and N/D1 interface and contacts the D1D2 barrel (PMID:26475856), and VIM and UBX elements that tether adjacent protomers (PMID:21822278); notably the UBX domain itself does not mediate p97 binding (PMID:19174149). Through these contacts UBXD1 acts as a potent ATPase inhibitor that drives asymmetric remodeling of the p97 hexamer into a ring-open conformation (PMID:21822278), and it competes with the p47 and Ufd1 adaptors for p97, thereby reconfiguring cofactor occupancy (PMID:19174149, PMID:19275885). Functionally, UBXD1 directs p97 to specific substrates and membranes: it targets mono-ubiquitylated caveolin-1 in endosomal high-molecular-weight complexes for endolysosomal degradation [#1-CAV1 context, #11], extracts the mitochondrial outer-membrane protein MCL1 (PMID:27913212), and—together with PLAA and the deubiquitinase YOD1 in the ELDR complex—removes K48-linked ubiquitin conjugates from damaged lysosomes to promote selective autophagy (PMID:27753622). It additionally modulates ERAD (regulating CFTR degradation) (PMID:19275885) and ERGIC-53 trafficking via direct N-terminal binding to the ERGIC-53 cytoplasmic tail (PMID:22337587). p97 disease mutations specifically disrupt the p97–UBXD1 complex and impair these pathways [#1-CAV1 context], and the p97/UBXD1 axis has been implicated in DYT1 dystonia-related nuclear envelope ubiquitin accumulation (PMID:35563018).

1. 2008 Medium

   Established that UBXD1 is an atypical p97 cofactor that binds p97 not through its UBX domain but through its PUB domain engaging the p97 C-terminus, defining a novel mode of cofactor attachment.

   Evidence Co-IP, in vitro binding, phosphorylation mutagenesis, and immunofluorescence in cells

   PMID:18656546

   Open questions at the time

   • Functional consequence of centrosomal enrichment not established
   • Physiological role of the ternary p47/UBXD1/p97 complex unresolved
2. 2009 Medium

   Resolved that UBXD1 binds p97 bipartitely—via the PUB domain at the C-terminus and a separate site that competes with p47 at the N-domain—providing a mechanism for cofactor exchange regulation.

   Evidence Biochemical binding assays, cell-based Co-IP, domain deletion analysis

   PMID:19174149

   Open questions at the time

   • Did not identify the N-domain-contacting segment structurally
   • Cellular substrate context not addressed
3. 2009 Medium

   Connected UBXD1 to ERAD by showing it can displace Ufd1 from p97 and that both its overexpression and depletion impair mutant CFTR degradation, framing it as a regulator of which adaptors load onto p97.

   Evidence Co-IP, gain- and loss-of-function with CFTR degradation assay

   PMID:19275885

   Open questions at the time

   • Mechanism of biphasic effect (both over- and under-expression impair) unexplained
   • Direct interaction with Derlin-1 not structurally mapped
4. 2011 High

   Identified the first physiological substrate-membrane context: p97/UBXD1 sorts mono-ubiquitylated caveolin-1 on endosomes for degradation, and showed p97 disease mutations selectively disrupt the p97-UBXD1 complex.

   Evidence Unbiased MS interactome, reciprocal Co-IP, siRNA with imaging, patient muscle tissue

   PMID:21822278

   Open questions at the time

   • Ubiquitin ligase generating CAV1 mono-ubiquitin not defined
   • How disease mutations alter complex geometry not shown structurally
5. 2012 Medium

   Extended UBXD1 function to secretory trafficking by showing its N-terminal residues bind the ERGIC-53 cytoplasmic tail in a p97-ATPase-dependent but ubiquitin-independent manner, modulating ERGIC-53 distribution.

   Evidence LC-MS/MS and SILAC interactome, Co-IP, p97/E1 inhibitor treatment, localization

   PMID:22337587

   Open questions at the time

   • Functional output of ERGIC-53 relocalization unclear
   • Role of Rab3GAP1/2 association undefined
6. 2015 High

   Mapped the disordered UBXD1 N-terminal region to the p97 N-domain/N-D1 interface and D1D2 barrel, providing a structural basis for ATPase inhibition and interdomain communication control.

   Evidence NMR titration, CD, fluorescence anisotropy, mutagenesis, ATPase and proteolysis assays

   PMID:26475856

   Open questions at the time

   • Did not capture the intact hexameric complex
   • Coupling of inhibition to substrate processing not addressed
7. 2016 High

   Defined the ELDR complex (UBXD1, PLAA, YOD1, p97) that strips K48-ubiquitin from damaged lysosomes downstream of K63-ubiquitin/p62, linking UBXD1 to selective autophagy of ruptured lysosomes.

   Evidence siRNA, Co-IP, immunofluorescence, LLOMe lysosomal damage, p97-mutant MEFs

   PMID:27753622

   Open questions at the time

   • Order of p97 recruitment relative to other ELDR subunits not fully resolved
   • How K48-removal triggers autophagosome formation mechanistically unclear
8. 2016 Medium

   Showed UBXD1 selects MCL1 for p97-mediated extraction from the mitochondrial outer membrane, expanding UBXD1 substrate specificity to mitochondrial membrane proteins in a disease context.

   Evidence Co-IP, RNAi, dominant-negative VCP, immunofluorescence in HD cell models

   PMID:27913212

   Open questions at the time

   • Ubiquitylation requirement for MCL1 extraction not defined
   • Generality beyond Huntington's disease context untested
9. 2019 Medium

   Determined the NMR structure of the UBXD1 PUB domain and its p97 C-terminal binding pocket, revealing conserved binding determinants with UBXD1-specific loop features.

   Evidence NMR structure determination, binding and mutational analysis

   PMID:31847414

   Open questions at the time

   • Functional importance of the unique loop/turn regions not established
   • PUB structure not placed in the context of the full complex
10. 2019 Low

    Confirmed UBXN6's role in caveolin-1 turnover in additional cell types and linked its loss to increased HIV-1 replication.

    Evidence siRNA, flow cytometry/IF for CAV1, in vitro HIV-1 replication assay

    PMID:31158522

    Open questions at the time

    • Single method per readout with no mechanistic placement of the HIV-1 effect
    • Whether CAV1 changes drive the HIV-1 phenotype not tested
11. 2022 Medium

    Implicated the p97/UBXD1 axis, independently of Ufd1/Npl4, in generating K48-ubiquitylated proteins sequestered in nuclear envelope herniations in Torsin-deficient cells, connecting it to DYT1 dystonia pathology.

    Evidence p97 inhibitor, UBXD1 and Ufd1/Npl4 knockdown, IF quantification of K48-ubiquitin in blebs

    PMID:35563018

    Open questions at the time

    • Direct substrates within blebs not identified
    • Causal contribution to dystonia phenotype not demonstrated in vivo
12. 2023 High

    Provided the integrated structural mechanism: cryo-EM of intact p97-UBXD1 shows VIM, UBX, and PUB domains tethering adjacent protomers and an N-terminal lariat wedging at interprotomer interfaces to drive asymmetric ring-opening and ATPase inhibition.

    Evidence Cryo-EM structure of intact complex, mutagenesis, in vitro ATPase assays

    PMID:37292947 PMID:37945741

    Open questions at the time

    • How ring-opening couples to substrate engagement and translocation not resolved
    • Conformational dynamics during active extraction not captured

• How UBXD1-driven hexamer ring-opening and ATPase inhibition are mechanistically converted into productive substrate extraction across its diverse membrane contexts (endosomes, mitochondria, lysosomes, ER) remains unresolved.
• No unifying model linking ATPase inhibition to substrate processing
• Substrate-specific recruitment determinants beyond CAV1/MCL1/ERGIC-53 undefined