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Structure paper

TitleStructural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 5340, Year 2021
Publish dateSep 9, 2021
AuthorsAnne-Xander van der Stel / Emily R Gordon / Arnab Sengupta / Allyson K Martínez / Dorota Klepacki / Thomas N Perry / Alba Herrero Del Valle / Nora Vázquez-Laslop / Matthew S Sachs / Luis R Cruz-Vera / C Axel Innis /
PubMed AbstractFree L-tryptophan (L-Trp) stalls ribosomes engaged in the synthesis of TnaC, a leader peptide controlling the expression of the Escherichia coli tryptophanase operon. Despite extensive ...Free L-tryptophan (L-Trp) stalls ribosomes engaged in the synthesis of TnaC, a leader peptide controlling the expression of the Escherichia coli tryptophanase operon. Despite extensive characterization, the molecular mechanism underlying the recognition and response to L-Trp by the TnaC-ribosome complex remains unknown. Here, we use a combined biochemical and structural approach to characterize a TnaC variant (R23F) with greatly enhanced sensitivity for L-Trp. We show that the TnaC-ribosome complex captures a single L-Trp molecule to undergo termination arrest and that nascent TnaC prevents the catalytic GGQ loop of release factor 2 from adopting an active conformation at the peptidyl transferase center. Importantly, the L-Trp binding site is not altered by the R23F mutation, suggesting that the relative rates of L-Trp binding and peptidyl-tRNA cleavage determine the tryptophan sensitivity of each variant. Thus, our study reveals a strategy whereby a nascent peptide assists the ribosome in detecting a small metabolite.
External linksNat Commun / PubMed:34504068 / PubMed Central
MethodsEM (single particle)
Resolution2.4 - 2.9 Å
Structure data

EMDB-12693, PDB-7o19:
Cryo-EM structure of an Escherichia coli TnaC-ribosome complex stalled in response to L-tryptophan
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-12694, PDB-7o1a:
Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophan
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-12695, PDB-7o1c:
Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome-RF2 complex stalled in response to L-tryptophan
Method: EM (single particle) / Resolution: 2.6 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-TRP:
TRYPTOPHAN / Tryptophan

ChemComp-HOH:
WATER / Water

ChemComp-K:
Unknown entry

Source
  • escherichia coli k-12 (bacteria)
  • escherichia coli (strain k12) (bacteria)
KeywordsTRANSLATION / ribosome / regulation / TnaC / arrest peptide / L-tryptophan / indole / stalling

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