Multi-scale classification decodes the complexity of the human E3 ligome
- Arghya Dutta
- Alberto Cristiani
- Siddhanta V. Nikte
- Jonathan Eisert
- Yves Matthess
- Borna Markusic
- Cosmin Tudose
- Chiara Becht
- Ronay Cetin
- Varun Jayeshkumar Shah
- Thorsten Mosler
- Koraljka Husnjak
- Ivan Dikic
- Manuel Kaulich
- Ramachandra M. Bhaskara
2025-12-25
E3 ubiquitin ligases are vital enzymes that define the ubiquitin code in cells. Beyond promoting protein degradation to maintain cellular health, they also mediate non-degradative processes like DNA repair, signaling, and immunity. Despite their therapeutic potential, a comprehensive framework for understanding the relationships among diverse E3 ligases is lacking. Here, we classify the “human E3 ligome”—an extensive set of catalytic human E3s—by integrating multi-layered data, including protein sequences, domain architectures, 3D structures, functions, and expression patterns. Our classification is based on a metric-learning paradigm and uses a weakly supervised hierarchical framework to capture authentic relationships across E3 families and subfamilies. It extends the categorization of E3s into RING, HECT, and RBR classes, including non-canonical mechanisms, successfully explains their functional segregation, distinguishes between multi-subunit complexes and standalone enzymes, and maps E3s to substrates and potential drug interactions. Our analysis provides a global view of E3 biology, opening strategies for drugging E3-substrate networks, including drug repurposing and designing specific E3 handles.