UBE2E1

UBE2E1 (UbcH6) is a human E2 ubiquitin-conjugating enzyme that catalyzes substrate ubiquitination both with dedicated RING/HECT E3 partners and, distinctively, in an E3-independent, substrate-sequence-dependent manner (PMID:8576257, PMID:38341401). Through its catalytic cysteine (Cys131) it forms ubiquitin thioester intermediates and transfers ubiquitin to a captured acceptor lysine; crystallographic analysis of UBE2E1 with the TRIM21 RING shows that coordination of the substrate lysine in the active site allosterically remodels the E2-E3 'linchpin' interface to couple substrate engagement to catalysis (PMID:31160341), while a complex with a SETDB1-derived peptide explains how UBE2E1 reads substrate sequence to transfer ubiquitin without an E3 (PMID:38341401). It serves as the in vivo E2 for PRC1-catalyzed monoubiquitination of histone H2A at Lys119, interacting with Ring1A/Ring1B to maintain Polycomb repression of the p16INK4a promoter and restrain cell growth (PMID:28073915), and partners with E3 ligases to ubiquitinate diverse substrates including TSSC5 (with RING105) (PMID:16314844) and β-catenin and the ciliopathy protein MKS1 (with RNF34), localizing with MKS1 at the ciliary base to control ciliary and Wnt signaling (PMID:35170427). UBE2E1 also directly ubiquitinates and drives degradation of ataxin-1, modulating its transcriptional repression and aggregation (PMID:18439907, PMID:18519031). Its abundance and activity are tightly regulated: USP7 binds the N-terminal ASTS motif to attenuate ubiquitination (PMID:23603909), OTUB1 non-catalytically suppresses UBE2E1 autoubiquitination to prevent its proteasomal degradation (PMID:30282802), and ISG15 conjugation at Lys136 blocks ubiquitin-thioester formation (PMID:16428300). UBE2E1 is enriched in slow-twitch muscle fibers where it protects against catabolic atrophy and engages the E3 MuRF1 in a substrate-dependent fashion (PMID:30453501).

1. 1996 Medium

   Established UBE2E1 as a bona fide human E2 enzyme by showing it engages a HECT-domain E3, while revealing it is functionally distinct from the better-known UbcH5.

   Evidence In vitro binding and reconstituted E1/E2/E3 ubiquitination assays with E6-AP and p53

   PMID:8576257

   Open questions at the time

   • Did not identify physiological substrates or cognate E3 partners
   • Weak activity with E6-AP left its productive E3 partnerships unknown
2. 2005 High

   Showed that UBE2E1 activity is switched off by post-translational modification, defining ISG15 conjugation as a regulatory brake on its enzymatic cycle.

   Evidence In vitro thioester formation assays with active-site mutagenesis and isolation of ISG15-modified UbcH6

   PMID:16428300

   Open questions at the time

   • The cellular ISG15 E3 ligase and trigger for UBE2E1 ISGylation not defined
   • Physiological consequences of suppressed activity not tested in vivo
3. 2006 Medium

   Identified a specific E3 partner (RING105) and substrate (TSSC5), demonstrating UBE2E1 builds polyubiquitin chains in a defined E2-E3 pairing.

   Evidence In vitro ubiquitination with site mapping and cellular expression with RING-finger mutant controls

   PMID:16314844

   Open questions at the time

   • Chain linkage type not characterized
   • Fate of ubiquitinated TSSC5 not established
4. 2008 Medium

   Revealed an E3-independent mode of action, showing UBE2E1 can bind and ubiquitinate a substrate directly and control its degradation.

   Evidence Yeast two-hybrid, Co-IP, co-localization, E3-free in vitro ubiquitination, and pulse-chase degradation of ataxin-1

   PMID:18439907 PMID:18519031

   Open questions at the time

   • Molecular basis of E3-free substrate recognition unresolved at the time
   • Polyglutamine-length-dependent resistance to degradation mechanism unclear
5. 2013 High

   Defined the N-terminal ASTS motif as a regulatory docking site, showing USP7 both binds and dampens UBE2E1 activity and sets its steady-state level.

   Evidence Reciprocal Co-IP, in vitro binding, ubiquitination assays, ASTS-deletion and USP7 catalytic mutants, cellular level analysis

   PMID:23603909

   Open questions at the time

   • Whether USP7 deubiquitinates UBE2E1 itself or its substrates not fully separated
   • Substrate-specific consequences of attenuation not mapped
6. 2017 High

   Placed UBE2E1 in a major chromatin pathway as the in vivo E2 for PRC1-mediated H2AK119 monoubiquitination, linking it to Polycomb repression and growth control.

   Evidence Co-IP with Ring1A/B, C131A dominant-negative and siRNA, p16 promoter ChIP, and growth assays in HCT116 cells

   PMID:28073915

   Open questions at the time

   • Genome-wide extent of UBE2E1-dependent H2AK119ub not defined
   • How UBE2E1 is selectively recruited to PRC1 versus other E3s unclear
7. 2018 High

   Identified OTUB1 as a non-catalytic stabilizer that prevents UBE2E1 self-destruction, establishing autoubiquitination as the route controlling its abundance.

   Evidence Otub1 knockout mice and cell lines, OTUB1 catalytic mutant, in vitro autoubiquitination, and proteasome-inhibitor rescue

   PMID:30282802

   Open questions at the time

   • Which downstream UBE2E1 functions are most sensitive to OTUB1 loss not resolved
   • Relationship between OTUB1 and USP7 control of UBE2E1 not integrated
8. 2018 Medium

   Assigned a tissue-specific physiological role, showing UBE2E1 is a slow-fiber-enriched protector against muscle atrophy that engages MuRF1.

   Evidence Fiber-type immunofluorescence, siRNA in C2C12 and in vivo muscle knockdown with cross-sectional area readouts

   PMID:30453501

   Open questions at the time

   • Direct ubiquitination substrates in muscle not identified
   • Mechanism by which UBE2E1 opposes rather than promotes atrophy unresolved
9. 2019 High

   Provided structural mechanism for E2-E3 catalysis, showing acceptor-lysine capture in the UBE2E1 active site allosterically activates the E3 interface.

   Evidence 2.82 Å crystal structure of TRIM21 RING-UBE2E1 with active-site mutagenesis and in vitro ubiquitination

   PMID:31160341

   Open questions at the time

   • Generality of the allosteric model across other E3 partners not tested structurally
   • Dynamics of the catalytic cycle beyond the captured-lysine state not resolved
10. 2022 High

    Connected UBE2E1 to ciliary biology and Wnt signaling through MKS1 and RNF34, with co-dependent stability between UBE2E1 and MKS1.

    Evidence Reciprocal Co-IP, ciliary-base co-localization, siRNA, in vitro/cellular ubiquitination of β-catenin and MKS1, and Mks1 knockout mouse

    PMID:35170427

    Open questions at the time

    • Distinction between regulatory and degradative MKS1 ubiquitination outcomes not fully mapped
    • How UBE2E1 is targeted to the ciliary base unknown
11. 2024 High

    Resolved the basis of E3-free ubiquitination, showing UBE2E1 reads substrate peptide sequence to transfer ubiquitin and enabling engineered ubiquitination chemistry.

    Evidence Crystal structure of UBE2E1 with a SETDB1-derived peptide, E3-free in vitro ubiquitination, and structure-guided engineering (SUE1)

    PMID:38341401

    Open questions at the time

    • Endogenous repertoire of sequence-dependent substrates not catalogued
    • Physiological prevalence of E3-free versus E3-dependent activity not quantified

• How the multiple regulators (USP7, OTUB1, ISG15) and dual E3-dependent/E3-free modes are integrated to determine which substrates UBE2E1 ubiquitinates in a given cell remains unresolved.
• No unified model of substrate selection across contexts
• Linkage-type specificity in vivo not systematically defined
• Tissue-specific substrate maps (e.g. muscle) absent