Crystal structure of the thermostable archaeal intron-encoded endonucleaseI-DmoI

I-DmoI is a 22 kDa endonuclease encoded by an intron in the 23 S rRNA gene of the hyperthermophilic archaeon Desulfurococcus mobilis. The structure of I-DmoI has been determined to 2.2 Angstrom resolution using multi-waveleng th anomalous diffraction techniques. I-DmoI, a protein of the LAGLIDADG mot if family, represents the first structure of a freestanding endonuclease wi th two LAGLIDADG motifs, and the first of a thermostable homing endonucleas e. I-DmoI consists of two similar alpha/beta domains (alpha beta beta alpha beta beta alpha) related by pseudo 2-fold symmetry. The LAGLIDADG motifs a re located at the carboxy-terminal end of the first alpha-helix of each dom ain. These helices form a two-helix bundle at the interface between the dom ains and are perpendicular to a saddle-shaped DNA binding surface, formed b y two four-stranded antiparallel beta-sheets. Despite substantially differe nt sequences, the overall fold of I-DmoI is similar to that of two other LA GLIDADG proteins for which the structures are known, I-CreI and the endonuc lease domain of PI-SceI. The three structures differ most in the loops conn ecting the beta-strands, relating to the respective DNA target site sizes a nd geometries. In addition, the absence of conserved residues surrounding t he active site, other than those within the LAGLIDADG motif, is of mechanis tic importance. Finally, the carboxy-terminal domain of I-DmoI is smaller a nd has a more irregular fold than the amino-terminal domain, which is more similar to I-CreI, a symmetric homodimeric endonuclease. This is reversed c ompared to PI-SceI, where the amino-terminal domain is more similar to carb oxy-terminal domain of I-DmoI and to I-CreI, with interesting evolutionary implications.