Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome

Science. 2012 Mar 16;335(6074):1370-2. doi: 10.1126/science.1217443.

Abstract

In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA(i)(fMet) and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Carboxylic Ester Hydrolases / chemistry*
  • Carboxylic Ester Hydrolases / metabolism*
  • Crystallography, X-Ray
  • Escherichia coli / chemistry*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism*
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Biosynthesis
  • Protein Structure, Tertiary
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / metabolism
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / metabolism
  • RNA, Transfer, Amino Acyl / chemistry
  • RNA, Transfer, Amino Acyl / metabolism
  • RNA, Transfer, Met / chemistry
  • RNA, Transfer, Met / metabolism
  • Ribosome Subunits, Large, Bacterial / chemistry
  • Ribosome Subunits, Large, Bacterial / metabolism
  • Ribosome Subunits, Small, Bacterial / chemistry
  • Ribosome Subunits, Small, Bacterial / metabolism
  • Ribosomes / chemistry*
  • Ribosomes / metabolism
  • Thermus thermophilus / chemistry*
  • Thermus thermophilus / metabolism
  • Thermus thermophilus / ultrastructure

Substances

  • Escherichia coli Proteins
  • RNA, Bacterial
  • RNA, Messenger
  • RNA, Ribosomal
  • RNA, Transfer, Amino Acyl
  • RNA, Transfer, Met
  • tRNA, peptidyl-
  • Carboxylic Ester Hydrolases
  • YaeJ protein, E coli

Associated data

  • PDB/4DH9
  • PDB/4DHA
  • PDB/4DHB
  • PDB/4DHC