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

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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 CX2, 4CX29–54[CH]X2, 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.