SNAP output for PDB entry 1njm [SNAP web server]

PDB-id

1njm; SNAP-derived features in text and JSON formats; DNAproDB

Class

ribosome

Method

X-ray (3.6 Å)

Summary

The crystal structure of the 50s large ribosomal subunit from deinococcus radiodurans complexed with a trna acceptor stem mimic (asm) and the antibiotic sparsomycin

Reference

Bashan A, Agmon I, Zarivatch R, Schluenzen F, Harms JM, Berisio R, Bartels H, Franceschi F, Auerbach T, Hansen HA, Kossoy E, Kessler M, Yonath A (2003): "Structural basis of the ribosomal machinery for Peptide bond formation, translocation, and nascent chain progression." Mol.Cell, 11, 91-102. doi: 10.1016/S1097-2765(03)00009-1.

Abstract

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.