Structural Basis for the Rescue of Stalled Ribosomes: Structure of YaeJ Bound to the Ribosome

• Published in: Science (American Association for the Advancement of Science) Vol. 335; no. 6074; pp. 1370 - 1372
• Main Authors: Gagnon, Matthieu G., Seetharaman, Sai V., Bulkley, David, Steitz, Thomas A.
• Format: Journal Article
• Language: English
• Published: Washington, DC American Association for the Advancement of Science 16.03.2012; The American Association for the Advancement of Science
• Subjects: 60 APPLIED LIFE SCIENCES; Amino Acid Sequence; BACTERIA; BASIC BIOLOGICAL SCIENCES; Biochemistry; Biological and medical sciences; Carboxylic Ester Hydrolases - chemistry; Carboxylic Ester Hydrolases - metabolism; Catalysis; Codons; Conformation; CRYSTAL STRUCTURE; Crystalline structure; Crystallography, X-Ray; Escherichia coli - chemistry; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Fundamental and applied biological sciences. Psychology; Gram-negative bacteria; HYDROLYSIS; Messenger RNA; Models, Molecular; Molecular biophysics; Molecular Sequence Data; Molecular structure; Nucleic Acid Conformation; Peptides; Protein Biosynthesis; Protein Structure, Tertiary; PROTEINS; Ribonucleic acid; Ribosome Subunits, Large, Bacterial - chemistry; Ribosome Subunits, Large, Bacterial - metabolism; Ribosome Subunits, Small, Bacterial - chemistry; Ribosome Subunits, Small, Bacterial - metabolism; RIBOSOMES; Ribosomes - chemistry; Ribosomes - metabolism; RNA; 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; SENSORS; Structure in molecular biology; Thermus thermophilus; Thermus thermophilus - chemistry; Thermus thermophilus - metabolism; Thermus thermophilus - ultrastructure; Transfer RNA; Thermus thermophilus; Bacteria; Molecular complex; Ribosome; Crystalline structure
• DOI: 10.1126/science.1217443
• ISSN: 0036-8075

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 Yae] bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNAi fMet and a short mRNA. The structure reveals that the C-terminal tail of Yae] 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 Yae] function and provides a basis for understanding how it rescues stalled ribosomes.