Abstract
The ribosome, the largest RNA-containing macromolecular machinery in cells, requires metal ions not only to maintain its three-dimensional fold but also to perform protein synthesis. Despite the vast biochemical data regarding the importance of metal ions for efficient protein synthesis and the increasing number of ribosome structures solved by X-ray crystallography or cryo-electron microscopy, the assignment of metal ions within the ribosome remains elusive due to methodological limitations. Here we present extensive experimental data on the potassium composition and environment in two structures of functional ribosome complexes obtained by measurement of the potassium anomalous signal at the K-edge, derived from long-wavelength X-ray diffraction data. We elucidate the role of potassium ions in protein synthesis at the three-dimensional level, most notably, in the environment of the ribosome functional decoding and peptidyl transferase centers. Our data expand the fundamental knowledge of the mechanism of ribosome function and structural integrity.
Highlights
The ribosome, the largest RNA-containing macromolecular machinery in cells, requires metal ions to maintain its three-dimensional fold and to perform protein synthesis
Ribosomes are conserved in all kingdoms of life: they are composed of rRNA and proteins unequally distributed among two asymmetric subunits[21]
Despite the vast biochemical data regarding the importance of metal ions for effective ribosome performance[25] and the increasing number of ribosome structures solved by X-ray crystallography or cryo-electron microscopy, the identification of metal ions within the ribosome remains elusive due to methodological limitations
Summary
The ribosome, the largest RNA-containing macromolecular machinery in cells, requires metal ions to maintain its three-dimensional fold and to perform protein synthesis. Functions and structures of biomolecules evolved in intracellular environments with K+ and Mg2+ among the predominant cations While both of these ions contribute to the stability of various RNA structures[14,15,16,17,18], together they demonstrate a more pronounced synergistic effect[19]. These two ions demonstrate significant differences in properties: Mg2+ is a small ion (ionic radius 0.72 Å)[20] with high charge density and strong preference of octahedral coordination (coordination number 6), while K+ is larger (ionic radius 1.51 Å)[20], less charged, leaning towards higher coordination numbers (8–12) This precludes their competition and expands the variety of environments and modes of possible interactions of these cations, which is crucial for macromolecular machines. None of the individual components, cations or polyamines, can entirely substitute for each other, and efficient translation by the ribosome can only be achieved by correct concentrations and balance between them
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