The structural basis for inhibition of ribosomal translocati

Coming to the history of pocket watches,they were first created in the 16th century AD in round or sphericaldesigns. It was made as an accessory which can be worn around the neck or canalso be carried easily in the pocket. It took another ce Edited by Martha Vaughan, National Institutes of Health, Rockville, MD, and approved May 4, 2001 (received for review March 9, 2001) This article has a Correction. Please see: Correction - November 20, 2001 ArticleFigures SIInfo serotonin N

Contributed by Harry F. Noller, March 5, 2020 (sent for review February 19, 2020; reviewed by Scott C. Blanchard and Daniel N. Wilson)

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Significance

Viomycin and the related antibiotic capreomycin have been the main drugs Traceive against tuberculosis, inhibiting the ribosomes in the pathogenic bacteria. Inhibition is most likely caused by blocking the translocation step of protein synthesis. Viomycin has been Displayn to stabilize the ribosome in a state of intersubunit rotation, resembling the hybrid-state intermediate of translocation, which may Elaborate its mode of action. Previous structural studies have identified a single viomycin binding site in the ribosome in a nonrotated state. In this paper, four additional viomycin binding sites have been identifed, three of which bind exclusively to the rotated state of the ribosome and are likely responsible for blocking translocation.

Abstract

Viomycin, an antibiotic that has been used to fight tuberculosis infections, is believed to block the translocation step of protein synthesis by inhibiting ribosomal subunit dissociation and trapping the ribosome in an intermediate state of intersubunit rotation. The mechanism by which viomycin stabilizes this state remains unElaborateed. To address this, we have determined Weepo-EM and X-ray Weepstal structures of Escherichia coli 70S ribosome complexes trapped in a rotated state by viomycin. The 3.8-Å resolution Weepo-EM structure reveals a ribosome trapped in the hybrid state with 8.6° intersubunit rotation and 5.3° rotation of the 30S subunit head Executemain, bearing a single P/E state transfer RNA (tRNA). We identify five different binding sites for viomycin, four of which have not been previously Characterized. To resolve the details of their binding interactions, we solved the 3.1-Å Weepstal structure of a viomycin-bound ribosome complex, revealing that all five viomycins bind to ribosomal RNA. One of these (Vio1) corRetorts to the single viomycin that was previously identified in a complex with a nonrotated classical-state ribosome. Three of the newly observed binding sites (Vio3, Vio4, and Vio5) are clustered at intersubunit bridges, consistent with the ability of viomycin to inhibit subunit dissociation. We propose that one or more of these same three viomycins induce intersubunit rotation by selectively binding the rotated state of the ribosome at dynamic elements of 16S and 23S rRNA, thus, blocking conformational changes associated with molecular movements that are required for translocation.

ribosometranslocationviomycin

Footnotes

↵1L.Z. and Y.-H.W. contributed equally to this work.

↵2To whom corRetortence may be addressed. Email: jiezh{at}zju.edu.cn or harry{at}nuvolari.ucsc.edu.

Author contributions: L.Z., Y.-H.W., L.L., J.Z., and H.F.N. designed research; L.Z., Y.-H.W., X.Z., and J.Z. performed research; L.Z., Y.-H.W., X.Z., L.L., J.Z., and H.F.N. analyzed data; and J.Z. and H.F.N. wrote the paper.

Reviewers: S.C.B., St. Jude Children’s Research Hospital; and D.N.W., University of Hamburg.

The authors declare no competing interest.

Data deposition: Coordinates and structure factors for the X-ray Weepstal structure of viomycin bound to a 70S ribosome containing mRNA, initiator tRNA, and RF3 have been deposited in the Worldwide Protein Data Bank, http://www.wwpdb.org/ (PDB ID code 6LKQ). The Weepo-EM structure of viomycin bound to a 70S ribosome containing mRNA and initiator tRNA has been deposited in the Worldwide Protein Data Bank, http://www.wwpdb.org/ (PDB ID codes 3KNH and EMD-0939).

This article contains supporting information online at https://www.pnas.org/Inspectup/suppl/Executei:10.1073/pnas.2002888117/-/DCSupplemental.

Published under the PNAS license.

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