The HECT1 family contains 20 E3s characterized by a C-terminal catalytic HECT domain (IPR000569) and one or two N-terminal domains. The HECT domain spans approximately 350 amino acids at the C-terminus and is structured into two lobes: the N-lobe and the C-lobe. The N-lobe is responsible for binding to the E2 enzyme-ubiquitin complex, which facilitates the transfer of ubiquitin from E2 to the C-lobe through a thioester intermediate involving a crucial catalytic cysteine. Once ubiquitin is appropriately positioned on the C-lobe, it is transferred to the target protein. Based on their N-terminal domains, the HECT family is categorized into three main subfamilies: NEDD4-like, HERC, and other HECT.
The "NEDD4-like" subfamily comprises 9 HECT proteins (NED4L, NEDD4, ITCH, WWP1-2, SMUF1-2, HECW1-2), mainly co-clustered according to sequence and domain architecture similarity, which feature the C2 (IPR000008) and WW (IPR001202) domains. The C2 domain aids in signal transduction and membrane trafficking in a calcium-dependent manner. It can also bind to phospholipids in a calcium-dependent manner, enabling membrane recruitment of the E3s. The WW domain contains two tryptophan residues, is involved in protein/protein interactions by recognizing proline-rich motifs (–PY– or –PPxY–) on target proteins, and is often associated with signal transduction proteins.
The other 11 E3s forming the HERC and other HECT subfamilies possess either a different N-terminal domain or none. The HERC subfamily contains four small HERC E3s with no N-terminus domain annotations, and they display high intra-subfamily similarity on every metric layer. The two larger HERC1 and HERC2 are co-clustered with the HECT2 family. The HERC proteins feature the (RLD) RCC1/BLIP II domain (IPR000408), known to act as a guanine-nucleotide dissociation stimulator, while HERC1 and HERC2 have other additional domains.
The other HECT subfamily contains HECT proteins with one or two different N-terminal domains. HECD3 contains the APC10/doc domain (IPR004939), which may facilitate ubiquitination reactions with other RING domains. UBE3A features an N-terminal Zn-binding domain, or AZUL domain (IPR032353), likely playing a role in substrate recognition. UBE3C and UBE3B feature an IQ motif. AREL1 possesses a Filamine/ABP280 repeat (IPR017868). The HACE1 includes Ankyrin repeats (IPR002110) common to protein–protein interaction motifs. HECD2 does not have any N-terminal domains. The enrichment analysis shows the association of the HECT1 family with biological processes such as regulation of dendrite morphogenesis, viral life cycle, and protein K-63 linked ubiquitination. The PDB contains 80 resolved structures that cover 13 of 20 HECT1 proteins.
Almost all HECT1 E3s are likely to function as standalone ligases; only four were found to operate as complex ligases. Analysis of the ESI network for this family revealed 270 unique E3-specific substrates and 433 family-specific substrates. SMUF1, SMUF2, and NEDD4 have E3 binders, which could be developed into lead compounds for E3 handle design.
For updated information and bibliography, please consult the supplementary information in Dutta et al. (2025, preprint)
The values represent E3 ligase confidence scores, calculated as the fraction of databases that annotate the protein as an E3 ligase (see preprint).
