tRNA Locations on the Ribosome

Nierhaus, Knud H.

doi:10.1002/3527603433.ch6

Cited by 4 publications

(3 citation statements)

References 19 publications

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“…The strong inhibition of the translation termination step by BlaS is noteworthy because no specific inhibitors of translation termination have been identified so far (2,(45)(46)(47). Some inhibitors of peptide bond formation have been shown to also inhibit peptide release (2), but none has been quantitatively demonstrated to inhibit the latter step to a greater degree than peptidyl transfer (48).…”

Section: Discussionmentioning

confidence: 99%

Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome

Svidritskiy

Ling

Ermolenko

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

107

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The antibiotic blasticidin S (BlaS) is a potent inhibitor of protein synthesis in bacteria and eukaryotes. We have determined a 3.4-Å crystal structure of BlaS bound to a 70S·tRNA ribosome complex and performed biochemical and single-molecule FRET experiments to determine the mechanism of action of the antibiotic. We find that BlaS enhances tRNA binding to the P site of the large ribosomal subunit and slows down spontaneous intersubunit rotation in pretranslocation ribosomes. However, the antibiotic has negligible effect on elongation factor G catalyzed translocation of tRNA and mRNA. The crystal structure of the antibiotic-ribosome complex reveals that BlaS impedes protein synthesis through a unique mechanism by bending the 3′ terminus of the P-site tRNA toward the A site of the large ribosomal subunit. Biochemical experiments demonstrate that stabilization of the deformed conformation of the P-site tRNA by BlaS strongly inhibits peptidyl-tRNA hydrolysis by release factors and, to a lesser extent, peptide bond formation.peptidyl transfer | ribosome crystal structure | termination inhibitor | translation inhibitor | translation termination T he growing problem of pathogen resistance to existing antibacterials prompts a search for alternative modes of inhibiting bacterial growth. The development of new drugs can be facilitated by understanding the mechanisms of action of known antibiotics (1). Because of its central role in cell metabolism, the ribosome is the target of numerous inhibitors that bind to various sites on the ribosome and interfere with different steps of protein synthesis. One of the predominant modes of action of ribosomal antibiotics is the inhibition of peptide bond formation. A majority of peptidyltransferase inhibitors, including the widely used antibacterials chloramphenicol, linezolid, and the lincosamides lincomycin and clindamycin, bind to the A site of the large ribosomal subunit at the peptidyl-transferase center of the ribosome (2-4). By contrast, blasticidin S (BlaS) binds to the P site of the large subunit (5) and inhibits the peptidyl-transferase reaction through a distinct mechanism, which is still poorly understood.BlaS, produced by some Streptomyces species, is a nucleoside analog consisting of a cytosine bonded to a pyranose ring and attached to an N-methyl-guanidine tail (Fig. 1A). BlaS has long been known to be a potent inhibitor of protein synthesis in bacteria and eukaryotes (6, 7). A crystal structure of the 50S subunit from Haloarcula marismortui bound to BlaS in the absence of tRNA revealed that BlaS occupies the P site of the large subunit (5). Two molecules of BlaS interact with the P loop and form base pairs with the universally conserved G2251 and G2252 of 23S ribosomal RNA (Escherichia coli 70S ribosome numbering is used throughout this article). These base pairing interactions closely mimic those of the two cytosine residues of the conserved CCA 3′ terminus of tRNA bound in the P site. Based on the finding that two molecules of BlaS mimic the cytosine residues of the...

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Section: Discussionmentioning

confidence: 99%

Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome

Svidritskiy

Ling

Ermolenko

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

107

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“…The P-site bound to the tRNA in the small 30S subunit is stabilized by A-minor type I and type II interactions between the 16S rRNA G1338 and A1339 and GC base pair 30-40 and 29-49 of the P-site tRNA (Abdi & Fredrick, 2005;Khatter et al, 2015). Residues A1339 and G1338 in the 16S rRNA Interact with the ASL (Anticodon Stem-Loop) of the P-site tRNA on one side and nucleotide 790 found at helix 24 of the 30S platform on the other side [34,41,42]. This ensures the tRNA does not move into the E-site.…”

Section: P-sitementioning

confidence: 99%

“…Overall, these tools improved the reliability and confidence in the results of in silico simulation and aided in the interpretation of the outcome of the simulation. The built model was further superimposed on the experimental crystal structure of the template and the root mean square deviation (RMSD) was calculated [41].…”

Section: Obtaining and Verifying Template Sequences And Three-dimensi...mentioning

confidence: 99%

Identification of Selected Kinetoplastids 18S rRNA Residues required for Efficient Recruitment of Initiator tRNA Met and AUG Selection in silico

Ndung’u,

Muge,

Wagacha

et al. 2023

Int J Bioinfor Intell Comput

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High Resolution 18S rRNA structures of kinetoplastids ribosomes from theoretical methods have provided atomic level details about the process of translation. This process entails detailed information on the mRNA and tRNA binding and decoding centers within the 18S rRNA that was previously not very well understood. We identified residues in selected kinetoplastids 18S rRNA critical in recruiting the first methionyl tRNA to the small ribosome subunit during initiation and comparing them to see the differences. The Kozak sequence presence on eukaryotic mRNAs tethers it to the AUG start codon. Kinetoplastids are a closely related group, and the three chosen exhibited differences in the A-site in terms of position and nucleotides found there. Interactions are found at the A-site (543-UUU-546 for T. cruzi, 560-CCUA-563 for T. brucei, and 540-UUUG-543 for Leishmania major), where the different mRNA get complementary sequences at the 16th helix. The current findings show that each messenger RNA has a sequence that is complementary to the appropriate 18S rRNA sequence, tethering the mRNA to the small ribosomal subunit, which then recruits the bigger subunit. When compared to the Kozak region that flanks the AUG start codon, this method effectively promotes start codon placement.

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Non‐Hydrolyzable RNA–Peptide Conjugates: A Powerful Advance in the Synthesis of Mimics for 3′‐Peptidyl tRNA Termini

et al. 2009

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Die Translation kleiner Peptide am Ribosom kann diesem eine Resistenz gegen Macrolidantibiotika verleihen. Zur Aufklärung dieses und ähnlicher Phänomene sind stabile RNA‐Peptid‐Konjugate, die Peptidyl‐tRNA imitieren, wünschenswert, besonders für die strukturbiologische Untersuchung von Ribosomen. Eine flexible Festphasensynthesestrategie macht diese Konjugate nun in effizienter Weise zugänglich, ohne Beschränkungen bezüglich der RNA‐ und Peptidsequenz.

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tRNA Locations on the Ribosome

Cited by 4 publications

References 19 publications

Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome

Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome

Identification of Selected Kinetoplastids 18S rRNA Residues required for Efficient Recruitment of Initiator tRNA Met and AUG Selection in silico

Non‐Hydrolyzable RNA–Peptide Conjugates: A Powerful Advance in the Synthesis of Mimics for 3′‐Peptidyl tRNA Termini

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