High-Resolution Structures of Large Ribosomal Subunits from Mesophilic Eubacteria and Halophilic Archaea at Various Functional States

Abstract

Structural analysis of the recently determined high resolution structures of the small and the large ribosomal subunits from three bacterial sources, assisted by the medium resolution structure of a complex of the entire ribosome with three tRNAs, led to a quantum jump in our understanding of the process of the translation of the genetic code into proteins. Results of these studies highlighted dynamic aspects of protein biosynthesis; illuminated the modes of action of several antibiotics; indicated strategies adopted by ribosomes for maximizing their functional activity and revealed a wealth of architectural elements, including long tails of proteins penetrating the particle s cores and stabilizing the intricate folds of the RNA chains. Binding of substrate analogues showed that the decoding and the peptide-bond formation are accomplished mainly by RNA. However, several proteins may be functionally relevant in directing the mRNA and in mediating the proper orientation of the tRNA molecules within the ribosomal rRNA frame. Elements involved in intersubunit contacts or in substrate binding are inherently flexible, but maintain well-ordered characteristic conformations in unbound particles. The ribosomes utilize this conformational variability for optimizing their efficiency and minimizing non-productive interactions, hence disorder of functionally relevant features may be linked to less active conformations or to far from physiological conditions. Clinically relevant antibiotics bind almost exclusively to rRNA. In the small subunit they affect the decoding accuracy or limit conformational mobility and in the large subunit they either interfere with substrate binding, by interacting with components of the peptidyl transferase cavity, or hinder the progression of the growing peptide chain.

Streptococcus pyogenes c-di-AMP Phosphodiesterase, GdpP, Influences SpeB Processing and Virulence

“…The ribosomal protein is a highly elongated protein containing two domains separated by a nine-turn connecting helix. In the crystal structure of Deinococcus radiodurance ribosomes [38], the location of Rpl9 is between the large subunit and the small subunit of the ribosome. Some studies showed that Rpl9 might be involved in translational fidelity.…”

Structure of the Ribosome

“…Also the L7/L12 stalk and the GTPase-associated center consisting of H42-H44 and proteins L7/L12 and L10 are shifted (by 3-4 Å) between D. radiodurans 50S and T. thermophilus 70S ribosome [1]. The helices H42-H44 show a rotation of about 12º in the case of the H. marismortui 50S (PDB 1JJ2) from its position in D. radiodurans 50S [19,48]. These observed flexibilities of the stalks are in line with cryo-EM studies of ribosome complexes in different functional states [49,50,24,51] H. marismortui 50S crystals derived according to Ban et al [11] were used in kinetic and crystallographic studies of the PTF reaction.…”

“…For example, the entire L1 stalk in the unbound D. radiodurans 50S is tilted by about 30º away from its position in the T. thermophilus 70S ribosome yielding a maximum distance of over 30 Å of the outermost points ( Fig. 2-3A) [19,48]. Also the L7/L12 stalk and the GTPase-associated center consisting of H42-H44 and proteins L7/L12 and L10 are shifted (by 3-4 Å) between D. radiodurans 50S and T. thermophilus 70S ribosome [1].…”

A Bright Future for Antibiotics?

“…Protein CTC is of particular interest because of its various molecular versions (see below and in Figure 5) and because it fills a gap between the central protuberance (CP) and the uL1 stalk, which is located adjacent to the A-site tRNA entrance corridor (12,123). The molecular compositions of the CTC protein (named after a general shock protein), as in D. radiodurans, exhibit evolutionary adaptation to environmental conditions.…”

“…The inherent flexibility of domain 3 may indicate that it serves as an A-site regulator and also somewhat influences the progression of the mRNA. Its interactions with the A-finger (A-site tRNA corridor), its capability to manipulate the binding of the A-site tRNA corridor, and the enhanced stability of the CP seem to provide a mechanism for survival under extremely stressful conditions, including hunger or minimal resources (123).…”