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
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Research Support, N.I.H., Extramural
MeSH terms
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Amino Acid Sequence
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Carboxylic Ester Hydrolases / chemistry*
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Carboxylic Ester Hydrolases / metabolism*
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Crystallography, X-Ray
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Escherichia coli / chemistry*
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Escherichia coli Proteins / chemistry*
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Escherichia coli Proteins / metabolism*
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Models, Molecular
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Molecular Sequence Data
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Nucleic Acid Conformation
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Protein Biosynthesis
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Protein Structure, Tertiary
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RNA, Bacterial / chemistry
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RNA, Bacterial / metabolism
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RNA, Messenger / chemistry
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RNA, Messenger / metabolism
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RNA, Ribosomal / chemistry
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RNA, Ribosomal / metabolism
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RNA, Transfer, Amino Acyl / chemistry
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RNA, Transfer, Amino Acyl / metabolism
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RNA, Transfer, Met / chemistry
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RNA, Transfer, Met / metabolism
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Ribosome Subunits, Large, Bacterial / chemistry
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Ribosome Subunits, Large, Bacterial / metabolism
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Ribosome Subunits, Small, Bacterial / chemistry
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Ribosome Subunits, Small, Bacterial / metabolism
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Ribosomes / chemistry*
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Ribosomes / metabolism
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Thermus thermophilus / chemistry*
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Thermus thermophilus / metabolism
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Thermus thermophilus / ultrastructure
Substances
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Escherichia coli Proteins
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RNA, Bacterial
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RNA, Messenger
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RNA, Ribosomal
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RNA, Transfer, Amino Acyl
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RNA, Transfer, Met
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tRNA, peptidyl-
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Carboxylic Ester Hydrolases
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YaeJ protein, E coli
Associated data
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PDB/4DH9
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PDB/4DHA
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PDB/4DHB
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PDB/4DHC