Mechanism of completion of peptidyltransferase centre assembly in eukaryotes

Elife. 2019 May 22;8:e44904. doi: 10.7554/eLife.44904.

Abstract

During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase centre (PTC) completion that explains how integration of the last ribosomal proteins is coupled to release of the nuclear export adaptor Nmd3. Single-particle cryo-EM reveals that eL40 recruitment stabilises helix 89 to form the uL16 binding site. The loading of uL16 unhooks helix 38 from Nmd3 to adopt its mature conformation. In turn, partial retraction of the L1 stalk is coupled to a conformational switch in Nmd3 that allows the uL16 P-site loop to fully accommodate into the PTC where it competes with Nmd3 for an overlapping binding site (base A2971). Our data reveal how the central functional site of the ribosome is sculpted and suggest how the formation of translation-competent 60S subunits is disrupted in leukaemia-associated ribosomopathies.

Keywords: S. cerevisiae; SBDS; Shwachman-Diamond syndrome; cryo-EM; leukaemia; molecular biophysics; ribosome; ribosomopathy; structural biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cryoelectron Microscopy
  • Peptidyl Transferases / metabolism*
  • Peptidyl Transferases / ultrastructure
  • RNA, Ribosomal / metabolism*
  • Ribosomal Proteins / metabolism*
  • Ribosome Subunits, Large, Eukaryotic / metabolism*
  • Ribosome Subunits, Large, Eukaryotic / ultrastructure
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae / ultrastructure

Substances

  • RNA, Ribosomal
  • Ribosomal Proteins
  • Peptidyl Transferases

Associated data

  • PDB/6RZZ
  • PDB/6S05
  • PDB/6QIK
  • PDB/6QTZ
  • PDB/6RI5
  • PDB/6QT0