1B24

I-DMOI, INTRON-ENCODED ENDONUCLEASE

Summary for 1B24

• Entry DOI: 10.2210/pdb1b24/pdb
• Descriptor: Homing endonuclease I-DmoI (2 entities in total)
• Functional Keywords: intron-encoded, endonuclease, homing, thermostable
• Biological source: Desulfurococcus mobilis
• Total number of polymer chains: 1
• Total formula weight: 22181.47

Authors

Van Roey, P.,Silva, G.H. (deposition date: 1998-12-03, release date: 1999-03-24, Last modification date: 2024-11-13)

Primary citation

Silva, G.H.,Dalgaard, J.Z.,Belfort, M.,Van Roey, P.
Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI.
J.Mol.Biol., 286:1123-1136, 1999

PubMed Abstract: 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 A resolution using multi-wavelength anomalous diffraction techniques. I-DmoI, a protein of the LAGLIDADG motif family, represents the first structure of a freestanding endonuclease with two LAGLIDADG motifs, and the first of a thermostable homing endonuclease. I-DmoI consists of two similar alpha/beta domains (alphabetabetaalphabetabetaalpha) related by pseudo 2-fold symmetry. The LAGLIDADG motifs are located at the carboxy-terminal end of the first alpha-helix of each domain. These helices form a two-helix bundle at the interface between the domains and are perpendicular to a saddle-shaped DNA binding surface, formed by two four-stranded antiparallel beta-sheets. Despite substantially different sequences, the overall fold of I-DmoI is similar to that of two other LAGLIDADG proteins for which the structures are known, I-CreI and the endonuclease domain of PI-SceI. The three structures differ most in the loops connecting the beta-strands, relating to the respective DNA target site sizes and geometries. In addition, the absence of conserved residues surrounding the active site, other than those within the LAGLIDADG motif, is of mechanistic importance. Finally, the carboxy-terminal domain of I-DmoI is smaller and has a more irregular fold than the amino-terminal domain, which is more similar to I-CreI, a symmetric homodimeric endonuclease. This is reversed compared to PI-SceI, where the amino-terminal domain is more similar to carboxy-terminal domain of I-DmoI and to I-CreI, with interesting evolutionary implications.

PubMed: 10047486
DOI: 10.1006/jmbi.1998.2519

Experimental method

X-RAY DIFFRACTION (2.2 Å)