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Structure paper

TitleStructural analysis of noncanonical translation initiation complexes.
Journal, issue, pagesJ Biol Chem, Vol. 300, Issue 10, Page 107743, Year 2024
Publish dateAug 31, 2024
AuthorsJacob M Mattingly / Ha An Nguyen / Bappaditya Roy / Kurt Fredrick / Christine M Dunham /
PubMed AbstractTranslation initiation is a highly regulated, multi-step process that is critical for efficient and accurate protein synthesis. In bacteria, initiation begins when mRNA, initiation factors, and a ...Translation initiation is a highly regulated, multi-step process that is critical for efficient and accurate protein synthesis. In bacteria, initiation begins when mRNA, initiation factors, and a dedicated initiator fMet-tRNA bind the small (30S) ribosomal subunit. Specific binding of fMet-tRNA in the peptidyl (P) site is mediated by the inspection of the fMet moiety by initiation factor IF2 and of three conserved G-C base pairs in the tRNA anticodon stem by the 30S head domain. Tandem A-minor interactions form between 16S ribosomal RNA nucleotides A1339 and G1338 and tRNA base pairs G30-C40 and G29-C41, respectively. Swapping the G30-C40 pair of tRNA with C-G (called tRNA M1) reduces discrimination against the noncanonical start codon CUG in vitro, suggesting crosstalk between the gripping of the anticodon stem and recognition of the start codon. Here, we solved electron cryomicroscopy structures of Escherichia coli 70S initiation complexes containing the fMet-tRNA M1 variant paired to the noncanonical CUG start codon, in the presence or absence of IF2 and the non-hydrolyzable GTP analog GDPCP, alongside structures of 70S initiation complexes containing this tRNA variant paired to the canonical bacterial start codons AUG, GUG, and UUG. We find that the M1 mutation weakens A-minor interactions between tRNA and 16S nucleotides A1339 and G1338, with IF2 strengthening the interaction of G1338 with the tRNA minor groove. These structures suggest how even slight changes to the recognition of the fMet-tRNA anticodon stem by the ribosome can impact the start codon selection.
External linksJ Biol Chem / PubMed:39222680
MethodsEM (single particle)
Resolution2.59 - 2.75 Å
Structure data

43929

9ax7

EMDB-43929, PDB-9ax7:
70S initiation complex (tRNA-fMet M1 + CUG start codon)
Method: EM (single particle) / Resolution: 2.63 Å

43930

9ax8

EMDB-43930, PDB-9ax8:
70S initiation complex (tRNA-fMet M1, initiation factor 2 + CUG start codon)
Method: EM (single particle) / Resolution: 2.6 Å

45569

9cg5

EMDB-45569, PDB-9cg5:
70S initiation complex (tRNA-fMet M1 + UUG start codon)
Method: EM (single particle) / Resolution: 2.59 Å

45572

9cg6

EMDB-45572, PDB-9cg6:
70S initiation complex (tRNA-fMet M1 + GUG start codon)
Method: EM (single particle) / Resolution: 2.61 Å

45573

9cg7

EMDB-45573, PDB-9cg7:
70S initiation complex (tRNA-fMet M1 + AUG start codon)
Method: EM (single particle) / Resolution: 2.75 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-IAS:
BETA-L-ASPARTIC ACID

ChemComp-GCP:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogue*YM

Source
  • escherichia coli (E. coli)
KeywordsRIBOSOME / translation initiation / tRNA-fMet M1 / frameshifting / initiation factor 2

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