The RING7 family consists of 27 RING E3s. This family has members with diverse Zn-finger domains, making it heterogeneous. This family is organized into seven distinct subfamilies.
The Lysine demethylase (KDM2) ligases subfamily is characterized by a distinctive multi-domain architecture featuring an N-terminal Jumonji C domain, CXXC-type and PHD-type Zn-finger domains, and a C-terminal F-box domain.
The ovarian tumor protease (OTU) E3 ligases form a separate subfamily, displaying the OTU and Zn-finger A20-type domains. They function as the deubiquitinase and ubiquitin modification enzymes in the NF-κB pathway.
The subfamily of Mind Bomb (MIB) ligase shows the presence of the N terminal MIB-herc2 domain, a Zn-finger ZZ-type domain followed by the MIB-herc2 domain, MIB SH3 repeat domains, and C-terminal Zn-finger RING domains.
The remaining four subfamilies contain many E3s with varied domain architectures and are named after well-known E3s within these sub-clusters. The "MARCH-like" subfamily contains 3 MARCH E3s and the other RNF proteins. These proteins share a Zn-finger RING-CH type catalytic domain. The three longer MARCH proteins (MARH6, MARH7, and MARHA/MARCH10) co-cluster within this family of large E3 ligases (~600 residues or longer).
MARH7 and MARHA lack transmembrane domains, while MARH6 contains several transmembrane domains orthologous to the yeast E3 ligase Doa10. This subfamily includes the Listerin (LTN1) ligase and two RNF proteins (RN139 and RN145). RN139 and RN145 are characterized by a TRC8-like N-terminal domain, encompassing 12 transmembrane domains and a putative sterol-sensing domain.
The "UNK-like" proteins constitute a distinct subfamily along with RNA-binding RC3H (ROQUIN) proteins. The characteristic feature of this subfamily is the presence of a Zn-finger CCCH-type domain. Within this subfamily, members cluster primarily based on domain composition similarity. RC3H proteins display a distinctive domain organization, featuring an N-terminal Zn-finger RING-type domain followed by a Roquin II domain and a C-terminal Zn-finger CCCH-type domain. The UNK-like ligases exhibit a unique architectural arrangement comprising an N-terminal Unkempt Zn-finger domain succeeded by multiple Zn-finger CCCH-type domain repeats.
The UHRF and JADE ligases form a separate subfamily ("UHRF-like"), distinguished by their Zn-finger PHD-type domains. UHRF family members possess a more intricate domain architecture, consisting of an N-terminal Ub-like domain, UHRF tandem tudor domain, Zn-finger PHD-type domain, and SRA-YDG domain—the latter mediating nucleic acid interactions—followed by a C-terminal Zn-finger RING-type domain. The functional roles of both the Zn-finger PHD-type and SRA-YDG domains are evidenced by enrichment in molecular functions, particularly histone-modifying activity and unmethylated CpG binding. The JADE ligases feature an N-terminal enhancer of a polycomb-like domain followed by a PHD-type domain.
The other heterogeneous subfamily, "UBE-like," contains 5 E3s and RNF31 (outlier, RBR-class). This subfamily shows the presence of different catalytic domains such as the U-box domain, Zinc finger, UBP-type, and Pep3/Vps18/deep orange. The E3 ligase UBE shows the presence of the Ubiquitin conjugation factor E4, core, and the U-box domain. The UBE proteins are involved in functions related to DNA damage.
Other family members, UBP33 and HDAC6, share a UBP-type Zn-finger domain, with UBP33 additionally containing ubiquitin-specific protease (USP) and DUSP domains. HDAC6 is distinguished by a histone deacetylase Zn-finger domain, which facilitates its histone modification function. VPS18 is characterized by a Pep3/Vps18/deep orange domain, which mediates trans-Golgi network trafficking.
The heterogeneity of these subfamilies is reflected in the family-level multiple sequence alignment, which exhibits numerous gaps. Functional enrichment analysis showed enrichment of RING7 members in the ERAD pathway, protein deubiquitination in ubiquitin-dependent protein catabolism, and B cell homeostasis.
Centrosomes and ubiquitin ligase complexes are enriched at the cellular component level with RING7 E3s. They mediate actin binding, unmethylated CpG binding, and modification-dependent protein binding functions. The PDB contains 142 structures covering 17 out of 27 RING7 proteins resolved in the PDB. We observed that seven proteins function as complexes, among which are FXL19, KDM2A, and KDM2B, all grouped in the KDM subfamily and probably serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex.
Most of the other RING7 family proteins are likely to function as standalone ligases, and the mode of action remains undetermined for six proteins. Analysis of the ESI network for this family revealed 109 unique E3-specific substrates and nine family-specific substrates. We identified ~5000 small molecule binders for HDAC6, distributed into a central large cluster organized into six well-distributed clusters. Small molecules targeting KDM proteins and RNF31 could also be observed.
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).
