Structural Basis of the Ribosomal Machinery for Peptide Bond Formation, Translocation, and Nascent Chain Progression

• Published in: Molecular cell Vol. 11; no. 1; pp. 91 - 102
• Main Authors: Bashan, Anat, Agmon, Ilana, Zarivach, Raz, Schluenzen, Frank, Harms, Joerg, Berisio, Rita, Bartels, Heike, Franceschi, Francois, Auerbach, Tamar, Hansen, Harly A.S, Kossoy, Elizaveta, Kessler, Maggie, Yonath, Ada
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 2003
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Catalytic Domain; Crystallography, X-Ray; Deinococcus - genetics; Models, Molecular; Molecular Structure; Nucleic Acid Conformation; Protein Biosynthesis; Protein Conformation; Protein Synthesis Inhibitors - chemistry; Protein Synthesis Inhibitors - metabolism; Puromycin - chemistry; Puromycin - metabolism; Ribosomal Proteins - chemistry; Ribosomal Proteins - genetics; Ribosomal Proteins - metabolism; RNA, Transfer, Amino Acyl - chemistry; RNA, Transfer, Amino Acyl - genetics; RNA, Transfer, Amino Acyl - metabolism; Sparsomycin - chemistry; Sparsomycin - metabolism
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/S1097-2765(03)00009-1

Crystal structures of tRNA mimics complexed with the large ribosomal subunit of Deinococcus radiodurans indicate that remote interactions determine the precise orientation of tRNA in the peptidyl-transferase center (PTC). The PTC tolerates various orientations of puromycin derivatives and its flexibility allows the conformational rearrangements required for peptide-bond formation. Sparsomycin binds to A2602 and alters the PTC conformation. H69, the intersubunit-bridge connecting the PTC and decoding site, may also participate in tRNA placement and translocation. A spiral rotation of the 3′ end of the A-site tRNA around a 2-fold axis of symmetry identified within the PTC suggests a unified ribosomal machinery for peptide-bond formation, A-to-P-site translocation, and entrance of nascent proteins into the exit tunnel. Similar 2-fold related regions, detected in all known structures of large ribosomal subunits, indicate the universality of this mechanism.