HEPNdomain

The HEPN domain is a conserved protein domain found across bacteria, archaea, and eukaryotes. The name stems from higher eukaryotes and prokaryotes nucleotide-binding, and the domain is most prominently associated with RNA cleavage activity. HEPN domains are often found in nucleases that participate in RNA metabolism, defense against phages, and regulatory toxin–antitoxin systems.

Biochemical properties and mechanism: The catalytic activity of HEPN-containing nucleases typically depends on dimerization, with the active site formed at the interface between two HEPN domains. A conserved motif, commonly including an arginine and a histidine (often described as an Rx4-6H motif), contributes to catalysis and substrate binding. The precise residues and their arrangement can vary among family members, but the dimeric interface is a recurring feature that enables RNA cleavage.

Distribution and roles: HEPN-domain proteins are widely distributed in prokaryotes and eukaryotes, and often occur as toxins in toxin–antitoxin modules, where RNA degradation inhibits cellular growth under stress. In CRISPR-Cend systems, the best-known example is Cas13, a Cas effector that contains two HEPN domains forming the RNase active site responsible for guide RNA–dependent RNA cleavage in immune defense. Other HEPN-containing proteins participate in diverse RNA-processing and antiviral responses and can function as standalone nucleases or as parts of larger multi-domain proteins.

Structure and evolution: The HEPN domain is typically about 150–180 amino acids in length and can appear as a single domain or as tandem repeats within a protein. Its presence in a broad range of life forms and in multiple functional contexts suggests an ancient and versatile RNA-targeting lineage, with diversification tied to organismal biology and defense strategies.