Helix 69: A Multitasking RNA Motif as a Novel Drug Target

Abstract

High‐resolution structures have shown that helix 69 (H69) of the large ribosomal subunit can assume variable conformational states during translation. Solution studies on small model RNAs, isolated subunits, and complete ribosomes also revealed a variety of H69 conformations. Specific nucleotides of H69 that undergo changes in their relative orientations within the ribosome structure play important roles in both translation and ribosome rescue. Furthermore, the presence of multiple pseudouridines influences the global conformational states of H69, and these highly conserved modifications play a role in regulating the positioning of key functional residues. Helix 69 has recently been identified as a novel antibiotic target site. Small molecules such as aminoglycosides bind to specific conformational states of H69 in bacterial ribosomes and affect the translation process. A variety of techniques have been employed to study H69, ranging from chemical synthesis to X‐ray crystallography, highlighting the importance of a detailed evaluation of the underlying principles of RNA conformational dynamics and drug targeting.

Structural Studies Reveal the Role of Helix 68 in the Elongation Step of Protein Biosynthesis

“…3C and D ). This movement appears particularly significant considering that H69, well-known for its flexibility ( 20 ), shows a displacement of only ∼15 Å both in the SA50S_50 and the SA70S_50 ( Fig. S4 ).…”

Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations

“…Formation of a canonical Watson–Crick base pair (Ψ1911–A1919), as well as a possible water-mediated hydrogen-bonding interaction involving Ψ1911N1H, helps maintain the stem duplex structure. These interactions allow conformational changes of H69, especially those in the loop region, during the highly dynamic translation process ( 73 ). Conformational changes that occur in the H69 ΨΨΨ loop as a result of the presence of the Ψ modifications at positions 1915 and 1917 are restricted to this region, while the stem structure is minimally perturbed ( 37 , 38 , 74 ).…”

Modulation of conformational changes in helix 69 mutants by pseudouridine modifications

“…Helix 69 plays important roles in the assembly of ribosomes and protein synthesis process [6]. Conservation of Ψ modifications at positions 1911, 1915, and 1917 are suggested to be correlated to their functions in modulating the structures and conformational behaviors of H69 [8, 17–21, 41, 44].…”

“…1), a 19-nucleotide hairpin located in domain IV of the 23S rRNA (large subunit RNA), establishes intersubunit bridge B2a with helix 44 (h44) of the 16S rRNA (small subunit RNA), and participates in the formation of intersubunit bridge B2b with helix 24 (h24) of the 16S rRNA [5]. Due to its central location in the ribosome, H69 is involved in almost every step of translation, in addition to ribosome rescue and antibiotic binding [6]. …”