TY - JOUR
T1 - Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation
AU - Basu, Ritwika
AU - Sherman, Michael B.
AU - Gagnon, Matthieu G.
N1 - Funding Information:
We thank members of the Gagnon laboratory for critical reading of the manuscript and suggestions. We are thankful to A. Miller for providing genomic DNA of the bacterium P. aeruginosa ; J. Miller and P. Leiman for their assistance with culturing and cell lysis of P. aeruginosa PAO1; the Sealy Center for Structural Biology and Molecular Biophysics of The University of Texas Medical Branch at Galveston for providing critical infrastructure and expertise; K.-Y. Wong and J. Perkyns for computational support, N. Prokhorov for help and advice with the RELION 3 software package, and Y. Polikanov for sharing his custom-made Python scripts. This work was supported by NIH grant R01GM136936 (to M.G.G.), The Welch Foundation grant H-2032-20200401 (to M.G.G.), startup funds from The University of Texas Medical Branch (to M.G.G.), Rising Science and Technology Acquisition and Retention Program award from the University of Texas system (to M.G.G.), Pilot Grant from the Institute for Human Infections and Immunity at The University of Texas Medical Branch (to M.G.G.), and NIH grant P41GM103311 (to the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco) for developing UCSF Chimera.
Funding Information:
We thank members of the Gagnon laboratory for critical reading of the manuscript and suggestions. We are thankful to A. Miller for providing genomic DNA of the bacterium P. aeruginosa; J. Miller and P. Leiman for their assistance with culturing and cell lysis of P. aeruginosa PAO1; the Sealy Center for Structural Biology and Molecular Biophysics of The University of Texas Medical Branch at Galveston for providing critical infrastructure and expertise; K.-Y. Wong and J. Perkyns for computational support, N. Prokhorov for help and advice with the RELION 3 software package, and Y. Polikanov for sharing his custom-made Python scripts. This work was supported by NIH grant R01GM136936 (to M.G.G.), The Welch Foundation grant H-2032-20200401 (to M.G.G.), startup funds from The University of Texas Medical Branch (to M.G.G.), Rising Science and Technology Acquisition and Retention Program award from the University of Texas system (to M.G.G.), Pilot Grant from the Institute for Human Infections and Immunity at The University of Texas Medical Branch (to M.G.G.), and NIH grant P41GM103311 (to the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco) for developing UCSF Chimera.
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - During translation initiation, initiation factor 2 (IF2) holds initiator transfer RNA (fMet-tRNAifMet) in a specific orientation in the peptidyl (P) site of the ribosome. Upon subunit joining IF2 hydrolyzes GTP and, concomitant with inorganic phosphate (Pi) release, changes conformation facilitating fMet-tRNAifMet accommodation into the P site and transition of the 70 S ribosome initiation complex (70S-IC) to an elongation-competent ribosome. The mechanism by which IF2 separates from initiator tRNA at the end of translation initiation remains elusive. Here, we report cryo-electron microscopy (cryo-EM) structures of the 70S-IC from Pseudomonas aeruginosa bound to compact IF2-GDP and initiator tRNA. Relative to GTP-bound IF2, rotation of the switch 2 α-helix in the G-domain bound to GDP unlocks a cascade of large-domain movements in IF2 that propagate to the distal tRNA-binding domain C2. The C2-domain relocates 35 angstroms away from tRNA, explaining how IF2 makes way for fMet-tRNAifMet accommodation into the P site. Our findings provide the basis by which IF2 gates the ribosome to the elongation phase.
AB - During translation initiation, initiation factor 2 (IF2) holds initiator transfer RNA (fMet-tRNAifMet) in a specific orientation in the peptidyl (P) site of the ribosome. Upon subunit joining IF2 hydrolyzes GTP and, concomitant with inorganic phosphate (Pi) release, changes conformation facilitating fMet-tRNAifMet accommodation into the P site and transition of the 70 S ribosome initiation complex (70S-IC) to an elongation-competent ribosome. The mechanism by which IF2 separates from initiator tRNA at the end of translation initiation remains elusive. Here, we report cryo-electron microscopy (cryo-EM) structures of the 70S-IC from Pseudomonas aeruginosa bound to compact IF2-GDP and initiator tRNA. Relative to GTP-bound IF2, rotation of the switch 2 α-helix in the G-domain bound to GDP unlocks a cascade of large-domain movements in IF2 that propagate to the distal tRNA-binding domain C2. The C2-domain relocates 35 angstroms away from tRNA, explaining how IF2 makes way for fMet-tRNAifMet accommodation into the P site. Our findings provide the basis by which IF2 gates the ribosome to the elongation phase.
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U2 - 10.1038/s41467-022-31129-2
DO - 10.1038/s41467-022-31129-2
M3 - Article
C2 - 35697706
AN - SCOPUS:85131819406
SN - 2041-1723
VL - 13
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 3388
ER -