Maintaining cellular order is a major logistical challenge: Individual mammalian cells contain billions of protein molecules, which must be synthesized, deployed, and removed with precision. In the ubiquitin-proteasome system (UPS), proteins destined for degradation are tagged with chains of several ubiquitin proteins and then degraded by the proteasome. The crucial step is the target selection: E3 ligases are enzymes that act as molecular "broker" by binding specific target proteins and coordinating the transfer of ubiquitin from an E2 enzyme.
As an E3 ligase recognizes only a restricted set of target proteins, cells maintain a large and diverse E3 ligase repertoire. A research team at Goethe University Frankfurt, led by Dr. Ramachandra M. Bhaskara from the Institute of Biochemistry II, has now compiled all members of the "broker family" in a catalog and mapped for the first time how human E3 ligases relate to one another, and what that implies for function, substrate recognition, and drug discovery.
A data-driven map of the "E3 ligome"
To describe the broker family - the so-called "E3 ligome" - the researchers performed AI-supported computational comparisons of E3 ligase features and then validated key functional inferences in cell culture experiments. In this way, the Frankfurt researchers defined 13 major families, as well as subfamilies, which capture more similarities between E3 ligase family members than shared amino acid sequences and structural characteristics. Bhaskara explains: "Our data-driven machine-learning approach reveals family-specific functions. For example, members of one family are important for DNA repair programs and for preventing unplanned cell death, while those of another are involved in antiviral defense."
Beyond their role in protein degradation, E3 ligases are also implicated in ubiquitin signaling, which is not used for protein degradation, broadening their relevance across cellular pathways and disease mechanisms.
Implications for next-generation therapeutics
The new E3 ligase map is particularly relevant for targeted protein degradation strategies used in novel types of active pharmaceutical substances such as PROTACs. PROTACs (Proteolysis Targeting Chimeras) are bifunctional molecules that bring an E3 ligase into proximity with a disease-relevant protein, triggering ubiquitin tagging and proteasomal destruction of the disease-relevant protein. Although the field has advanced rapidly, most existing PROTAC programs rely on only a small number of well-characterized E3 ligases.
By systematically analyzing the full E3 ligome, the team identified 40 additional E3 ligases that may be suitable for PROTAC development-and, importantly, the family relationships may help researchers repurpose or adapt ligands and design principles across related E3 ligases. This could widen the range of tissues, cellular contexts, and diseases that targeted degradation can reach.
Open resource for the research community
Because many groups worldwide are developing targeted degradation approaches, the Goethe University team has made the complete E3 ligome publicly available via a dedicated database, enabling other researchers to build on the classification and functional insights.
Publication: Arghya Dutta, Alberto Cristiani, Siddhanta V. Nikte, Jonathan Eisert, Yves Matthess, Borna Markusic, Cosmin Tudose, Chiara Becht, Varun Jayeshkumar Shah, Thorsten Mosler, Koraljka Husnjak, Ivan Dikic, Manuel Kaulich, Ramachandra M. Bhaskara: Multi-scale classification decodes the complexity of the human E3 ligome. Nature Communications (2025) https://doi.org/10.1038/s41467-025-67450-9
Picture download:
https://www.uni-frankfurt.de/181983680
Captions:
1.Sun of families: Researchers at Goethe University have elucidated the relationships among all 462 catalytic human E3 ligases; E3 ligases also support non-degradative functions. Image: Ramachandra M. Bhaskara, Goethe University Frankfurt
2. PROTACs and E3 ligases: PROTACs link a target protein (protein of interest, POI) with an E3 ligase, which mediates the ubiquitin labeling (yellow) of the POI via an E2 enzyme. The POI is then degraded in the proteasome shredder (blue). Image: Institute of Biochemistry II, Goethe University Frankfurt
