STRUCTURAL FEATURES OF THE BINDING-SITE FOR RIBOSOMAL-PROTEIN SS IN ESCHERICHIA-COLI 16S RIBOSOMAL-RNA DEFINED USING NMR-SPECTROSCOPY

Ribosomal protein S8 of Escherichia coli plays a key role in 30S ribos omal subunit assembly through its interaction with 16S rRNA, S8 also p articipates in the translational regulation of ribosomal protein expre ssion through its interaction with spe operon mRNA, The binding site f or protein S8 within the 16S rRNA encompasses nucleotides G588 to G604 and C634 to C651 and is composed of two base paired helical regions t hat flank a phylogenetically conserved core element containing nine re sidues. We have investigated the structure of the rRNA binding site fo r S8 both in the free state and in the presence of protein using NMR s pectroscopy. The integrity of the two helical segments has been verifi ed, and the presence of G597 . C633 and A596 . U644 base pairs within the conserved core, predicted from comparative analysis, have been con firmed. In addition, we have identified a base triple within the core that is composed of residues A595 .(A596 . U644). The NMR data suggest that S8-RNA interaction is accomplished without significant changes i n the RNA. Nonetheless, S8 binding promotes formation of the U598 . A6 4O base pair and appears to stabilize the G597 . C643 and A596 . U644 base pairs.