Ribosome, High Resolution Structure and Function

Abstract

The code for the amino acid sequence of proteins is translated by the ribosome using messenger RNA as the template. Ribosomes are RNA-protein complexes built of two subunits. In prokaryotes, the ribosome consists of a large 50S and a small 30S ribosomal subunit. Both subunits together form the 70S ribosome, the prokaryotic translation machinery. Structures of both ribosomal subunits have been solved at near-atomic resolution. The large ribosomal subunits are from the halophilic archaebacterium Haloarcula marismortui and from the eubacterium Deinococcus radiodurans . The small subunit has been solved from the thermophilic eubacterium Thermus thermophilus . Structures of the ribosomal subunits were also determined in complex with various antibiotics, substrate analogs, and two translation initiation factors. Finally, the entire 70S ribosome from T. thermophilus with mRNA and tRNAs is available at 5.5 A as a molecular model. This wealth of structural data allows for a detailed understanding of the molecular mechanism of peptide synthesis by the ribosome. The two most important steps in protein synthesis are the recognition of the cognate aminoacyl-tRNA and the peptidyl transfer reaction. These two functions are allotted to the two subunits of the ribosome. The small subunit mediates the interactions between tRNAs and the mRNA and selects for the correct tRNA in the decoding center. The large subunit comprises the peptidyl transferase center and provides the exit tunnel for the growing nascent polypeptide chain. The crystal structures of the separated subunits reveal many mechanistic details of the peptidyl transfer and decoding. The structures show unequivocally that mainly ribosomal RNA is present in the peptidyl transferase center as well as in the decoding center, indicating that it is in fact ribosomal RNA that is responsible for all aspects of peptide synthesis. In other words, the ribosome is a ribozyme. Here, we analyze the crystal structures of prokaryotic 50S and 30S subunits and the intact 70S ribosome with respect to their function and describe how our understanding of the mechanism of translation has been influenced by these recent structures. Furthermore, we outline the impact of cryo-electron microscopic studies (cryoEM) on our knowledge of ribosome conformational flexibility and ribosome complexes with translation factors. Keywords: Codon and Anticodon; Decoding; Elongation Factors; Exit Tunnel; Initiation Factors; Molecular Chaperones; Nascent Peptide; Peptidyl Transferase Reaction; Release Factors; Translocation; Translocation Machinery