The RING3 family comprises 28 RING ligases organized into five distinct subfamilies. This family is characterized by a prominent C-terminal Zn-finger RING-type catalytic domain. The multiple sequence alignment (MSA) of the RING3 family demonstrates the conservation of the RING domain across all E3 ligases in this family.
The first subfamily consists of nine Ring finger (RNF) ligases that contain the protease-associated (PA) domain (IPR003137), forming a characteristic lid-like structure involved in protein-protein interactions.
The four MEX ligases cluster into a separate subfamily, distinguished by the presence of an N-terminal RNA-binding K-homology domain (IPR004087).
The third subfamily encompasses four BIRC ligases that contain the baculoviral IAP repeat (BIR) domain. A notable exception among the BIRC proteins is BIRC7, which lacks the BIR1/2 domain and co-clusters with the RING4 family. XIAP (BIRC4) plays a crucial regulatory role in programmed cell death within this subfamily.
Another smaller subfamily contains Neuralized-like (NEURL) ligases featuring the Neuralized homology repeat (NHR) domain (IPR006573), which facilitates development in the central and peripheral nervous systems.
The last subfamily includes the oncoprotein MDM2 and its homologs (MDM4), along with other proteins possessing a C-terminal RING-type domain (RFFL, RNF34, MUL1, MYLIP, RNF26, and CGRF).
The RING3 family demonstrates significant functional segregation. It is strongly associated with regulating nucleotide-binding, leucine-rich repeat-containing receptor signaling pathways, response to biotic stimuli, and pattern recognition receptor signaling pathways.
RING3 proteins are primarily associated with the late endosome at the cellular component level. They are enriched in molecular functions such as Cys-type endopeptidase inhibitor activity in the apoptotic process, p53 binding, and ubiquitin ligase activity.
The PDB contains approximately 291 structures covering 14 out of 28 RING3 proteins. Most proteins in the RING3 family are likely to function as standalone E3 ligases, while only two proteins are presumed to operate as part of a complex. Analysis of the ESI network for this family revealed 312 unique E3-specific substrates and 25 family-specific substrates. MDM2, MDM4, XIAP, BIRC2, BIRC3, and BIRC8 extensively targeted by PROTACs and existing E3 binders. The MDM2 binding compounds occupy a large chemical space. Several E3 handles developed are cross-reactive and interact with other family members, indicating similarities in their binding sites.
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).
