Detailed analysis of RNA-protein interactions within the ribosomal proteinS8-rRNA complex from the archaeon Methanococcus jannaschii

The crystal structure of ribosomal protein S8 bound to its target 16 S rRNA from a hyperthermophilic archaeon Methanococcus jannaschii has been determ ined at 2.6 Angstrom resolution. The protein interacts with the minor groov e of helix H21 at two sites located one helical turn apart, with S8 forming a bridge over the RNA major groove. The specificity of binding is essentia lly provided by the C-terminal domain of S8 and the highly conserved nucleo tide core, characterized by two dinucleotide platforms, facing each other. The first platform (A595-A596), which is the less phylogenetically and stru cturally constrained, does not directly contact the protein but has an impo rtant shaping role in inducing cross-strand stacking interactions. The seco nd platform (U641-A642) is specifically recognized by the protein. The univ ersally conserved A642 plays a pivotal role by ensuring the cohesion of the complex organization of the core through an array of hydrogen bonds, inclu ding the G597-C643.U641 base triple, In addition, A642 provides the unique base-specific interaction with the conserved Ser105, while the Thr106 - Thr 107 peptide link is stacked on its purine ring. Noteworthy, the specific re cognition of this tripeptide (Thr-Ser-Thr/Ser) is parallel to the recogniti on of an RNA tetraloop by a dinucleotide platform in the P4-P6 ribozyme dom ain of group I intron. This suggests a general dual role of dinucleotide pl atforms in recognition of RNA or peptide motifs. One prominent feature is t hat conserved sidechain amino acids, as well as conserved bases, are essent ially involved in maintaining tertiary folds. The specificity of binding is mainly driven by shape complementarity, which is increased by the hydropho bic part of side-chains. The remarkable similarity of this complex with its homologue in the T. thermophilus 30 S subunit indicates a conserved intera ction mode between Archaea and Bacteria. (C) 2001 Academic Press.