UBE2E1

UBE2E1 (UbcH6) is a ubiquitin-conjugating E2 enzyme that functions with diverse RING and HECT E3 ligases—and also independently of E3 ligases—to ubiquitinate substrates including histone H2A at Lys-119, β-catenin, ataxin-1, TSSC5, MKS1, and SETDB1, thereby participating in Polycomb-mediated gene silencing, ciliary Wnt/β-catenin signaling, and protein homeostasis (PMID:28073915, PMID:35170427, PMID:18439907, PMID:38341401). Its unique N-terminal extension contains an ASTS motif that mediates binding to the deubiquitinase USP7, which stabilizes UBE2E1 levels and modulates its ubiquitination output, while OTUB1 non-catalytically prevents UBE2E1 autoubiquitination and proteasomal degradation (PMID:23603909, PMID:30282802). UBE2E1 activity is negatively regulated by ISG15 conjugation at Lys136 near its catalytic cysteine, linking the interferon-stimulated ISG15 pathway to ubiquitin conjugation (PMID:16428300). Structural studies reveal that substrate lysine enters the UBE2E1 active site through a trajectory distinct from canonical SUMO-targeted mechanisms, and that UBE2E1 possesses intrinsic peptide-sequence-dependent substrate recognition enabling E3-independent ubiquitination (PMID:31160341, PMID:38341401).

1. 1996 High

   Establishing UBE2E1 as a functional ubiquitin-conjugating enzyme with selective E3 partnerships resolved its enzymatic identity: UBE2E1 cooperates with the HECT E3 E6-AP but not RSP5, indicating intrinsic selectivity among E3 partners.

   Evidence In vitro ubiquitination reconstitution with multiple E2/E3 combinations and protein-protein interaction assays

   PMID:8576257

   Open questions at the time

   • Range of physiological E3 partners unknown
   • No cellular substrates identified
   • No structural basis for E3 selectivity
2. 2005 High

   Demonstrating that ISG15 conjugation at Lys136 suppresses UBE2E1 ubiquitin E2 activity revealed a regulatory crosstalk mechanism between the ISG15 and ubiquitin conjugation systems.

   Evidence In vitro ISGylation assay with site-directed mutagenesis and thioester intermediate detection

   PMID:16428300

   Open questions at the time

   • Physiological contexts in which ISGylation regulates UBE2E1 not defined
   • Effect of ISGylation on specific substrate ubiquitination not tested
3. 2006 High

   Identifying UBE2E1 as the E2 for the RING E3 RING105 in ubiquitinating TSSC5 established UBE2E1 function with RING-type E3 ligases and linked it to cell cycle regulation.

   Evidence In vitro ubiquitination reconstitution with RING105 active-site mutant controls and cellular overexpression

   PMID:16314844

   Open questions at the time

   • Endogenous RING105–UBE2E1 complex not validated
   • TSSC5 ubiquitination sites not mapped
4. 2008 Medium

   Showing that UBE2E1 ubiquitinates ataxin-1 independently of an E3 ligase and regulates its proteasomal degradation and aggregate formation established a direct role in neurodegenerative protein homeostasis.

   Evidence Yeast two-hybrid, reciprocal Co-IP, in vitro E3-free ubiquitination, and transcriptional repression/aggregate assays in mammalian cells

   PMID:18439907 PMID:18519031

   Open questions at the time

   • In vivo relevance in SCA1 mouse models not tested
   • Mechanism of E3-independent substrate recognition unknown at this point
   • Single laboratory findings
5. 2013 High

   Identifying USP7 as a binding partner and regulator of UBE2E1 through the N-terminal ASTS motif revealed a deubiquitinase-dependent mechanism that maintains UBE2E1 protein levels and attenuates its ubiquitination activity.

   Evidence In vitro and in vivo Co-IP, reconstituted ubiquitination with USP7 catalytic mutants, knockdown/overexpression cellular assays

   PMID:23603909

   Open questions at the time

   • Structural basis of ASTS motif recognition by USP7 not resolved
   • Whether USP7 regulation is constitutive or signal-dependent unknown
6. 2017 High

   Demonstrating that UBE2E1 is a critical E2 for PRC1-mediated histone H2A Lys-119 monoubiquitination placed UBE2E1 in Polycomb-mediated transcriptional repression and connected USP7 regulation of UBE2E1 to epigenetic gene silencing.

   Evidence Co-IP with Ring1A/Ring1B, C131A catalytic mutant, shRNA knockdown, ChIP at p16INK4a promoter

   PMID:28073915

   Open questions at the time

   • Whether UBE2E1 is the sole or dominant E2 for PRC1 in all cell types not established
   • Genome-wide H2AK119ub changes upon UBE2E1 loss not profiled
7. 2018 High

   Establishing that OTUB1 non-catalytically stabilizes UBE2E1 by blocking autoubiquitination—with Otub1 knockout mice showing embryonic lethality and UBE2E1 destabilization—defined a second deubiquitinase-dependent regulatory axis for UBE2E1 protein homeostasis.

   Evidence Otub1 knockout mouse and cell lines, in vitro autoubiquitination assay, catalytic vs. binding mutant controls

   PMID:30282802

   Open questions at the time

   • Relative contribution of UBE2E1 destabilization to Otub1 knockout lethality not isolated
   • Other E2 enzymes stabilized by OTUB1 not fully surveyed
8. 2018 Medium

   Localizing UBE2E1 to slow-twitch muscle fibers and showing that its knockdown exacerbates dexamethasone-induced atrophy revealed a tissue-specific protective role in skeletal muscle mass maintenance.

   Evidence Fiber-type immunofluorescence, shRNA knockdown in C2C12 myotubes and mouse tibialis anterior, dexamethasone atrophy model

   PMID:30453501

   Open questions at the time

   • UBE2E1 substrates mediating muscle protection not identified
   • Fiber-type restriction mechanism unknown
   • Single study without genetic knockout validation
9. 2019 High

   Solving the crystal structure of the TRIM21 RING–UBE2E1 complex with a substrate lysine captured in the active site revealed the allosteric activation mechanism and showed that substrate lysine entry differs from canonical SUMO-targeted ubiquitination.

   Evidence X-ray crystallography at 2.82 Å, active-site mutagenesis, in vitro ubiquitination reconstitution, SAXS

   PMID:31160341

   Open questions at the time

   • How E3-independent substrate recognition compares structurally was unresolved
   • Dynamics of allosteric activation not captured
10. 2022 High

    Placing UBE2E1 at the ciliary base in complex with MKS1 and RNF34, where it polyubiquitinates β-catenin and controls MKS1 stability, established UBE2E1 as a regulator of ciliary Wnt/β-catenin signaling.

    Evidence Co-IP, colocalization, siRNA knockdown, in vitro ubiquitination, Wnt reporter assay, Mks1 knockout mouse epistasis

    PMID:35170427

    Open questions at the time

    • Whether UBE2E1 directly ubiquitinates β-catenin at cilia or acts through MKS1 not fully dissected
    • Ciliopathy patient mutations in UBE2E1 not reported
11. 2024 High

    Solving the crystal structure of UBE2E1 bound to a SETDB1-derived substrate peptide revealed that UBE2E1 performs E3-independent ubiquitination through peptide-sequence-dependent active-site recognition, providing a structural basis for its unusual E3-free activity.

    Evidence X-ray crystallography of UBE2E1–peptide complex, E3-free in vitro ubiquitination, mutagenesis, chemical protein synthesis

    PMID:38341401

    Open questions at the time

    • Scope of endogenous substrates recognized by this E3-free mechanism unknown
    • Whether E3-independent activity is regulated in vivo not addressed

• It remains unknown how UBE2E1's E3-dependent and E3-independent activities are partitioned among its diverse substrates in vivo, what signals dictate the choice between mono- and polyubiquitination, and whether UBE2E1 contributes to human ciliopathy or neurodegenerative disease.
• Systematic identification of endogenous UBE2E1 substrates lacking
• Chain-type specificity (K48 vs K63 vs monoubiquitin) across different E3 partnerships not comprehensively defined
• No human disease-causing mutations reported