Crystal structure of pre-ribosomal RNA processing factor Dim2p from Pyrococcus horikoshii OT3 and its interaction with ribosomal RNA

Department of Applied Biological Chemistry, University of Tokyo
â—‹Min Ze Jia Jun Otsuka Woo Cheol Lee Koji Nagata Masaru Tanokura

The eukaryotic rRNA processing factor Dim2p is required for the cleavage of rRNA precursors at processing sites A2 to generate the pre-20S rRNA. Its homologs are distributed from archaea to metazoa. In this study, we have solved the crystal structure of PH-Dim2p (Dim2p from Pyrococcus horikoshii OT3) at 2.0-Å resolution. The PH-Dim2p molecule contains two KH domains, KH-1 and KH-2, which have dissimilar molecular surfaces in terms of electrostatic potentials. Binding assays have shown that PH-Dim2p shows no sequence preference in target rRNA molecules and that only KH-1 binds 16S rRNA while KH-2 does not. Based on the crystal structure of PH-Dim2p and the binding assay data, we have constructed a putative model of the PH-Dim2p and ribosomal RNA complex.