Self‐splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family

Abstract

A new family of protein domains consisting of 50–80 amino acid residues is described. It is composed of nearly 40 members, including domains encoded by plastid and phage group I introns; mitochondrial, plastid, and bacterial group II introns; eubacterial genomes and plasmids; and phages. The name “EX₁H‐HX₃H” was coined for both domain and family. It is based on 2 most prominent amino acid sequence motifs, each encompassing a pair of highly conserved histidine residues in a specific arrangement: EX₁HH and HX₃H. The “His” motifs often alternate with amino‐ and carboxy‐terminal motifs of a new type of Zn‐finger‐like structure CX_{2, 4}CX_29–54[CH]X_{2, 3}[CH]. The EX₁HH‐HX₃H domain in eubacterial E2‐type bacteriocins and in phage RB3 (wild variant of phage T4) product of the nrdB group I intron was reported to be essential for DNA endonuclease activity of these proteins. In other proteins, the EX₁HH‐EX₃H domain is hypothesized to possess DNase activity as well. Presumably, this activity promotes movement (rearrangement) of group I and group II introns encoding the EX₁HH‐HX₃H domain and other gene targets. In the case of Escherichia coli restrictase McrA and possibly several related proteins, it appears to mediate the restriction of alien DNA molecules.