ArticleNucleic acids research2005
Independent binding sites of small protein B onto transfer-messenger RNA during trans-translation.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 30 citations in OpenAlex.
- In vivo tmRNA protection by SmpB and pre-ribosome binding conformation in solution.RNA (New York, N.Y.) · 2014Article
- The tmRNA ribosome-rescue system.Advances in protein chemistry and structural biology · 2012Review
- SmpB contributes to reading frame selection in the translation of transfer-messenger RNA.Journal of molecular biology · 2009Article
- Escherichia coli tmRNA lacking pseudoknot 1 tags truncated proteins in vivo and in vitro.RNA (New York, N.Y.) · 2009Article
- The highest affinity binding site of small protein B on transfer messenger RNA is outside the tRNA domain.RNA (New York, N.Y.) · 2008Article
- The role of upstream sequences in selecting the reading frame on tmRNA.BMC biology · 2008Article
- Making the jump: new insights into the mechanism of trans-translation.Journal of biology · 2008Review
- Functional SmpB-ribosome interactions require tmRNA.The Journal of biological chemistry · 2007Article
- A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation.RNA (New York, N.Y.) · 2007Article
- Structure probing of tmRNA in distinct stages of trans-translation.RNA (New York, N.Y.) · 2007Article
- Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.The Journal of biological chemistry · 2007Article
- Interaction of SmpB with ribosome from directed hydroxyl radical probing.Nucleic acids research · 2007Article
- Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation.Nucleic acids research · 2006Article
- Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation.Nucleic acids research · 2006Article
- Deacylated tRNA is released from the E site upon A site occupation but before GTP is hydrolyzed by EF-Tu.Nucleic acids research · 2005Article
- Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA.Nucleic acids research · 2005Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Stalled bacterial ribosomes are freed by transfer-messenger RNA (tmRNA). With the help of small protein B (SmpB), protein synthesis restarts and tmRNA adds a tag to the stalled protein for destruction. The conformation of a 347 nt long tmRNA from a thermophile and its interactions with SmpB were monitored using structural probes. The RNA is highly folded, including the reading frame, with <30% of unpaired residues. Footprints between SmpB and tmRNA are in the elbow of the tRNA domain, in some pseudoknots including one essential for function and in the lower part of the stem exiting the tRNA domain. The footprints outside the tRNA domain are scattered onto the tmRNA sequence, but form a cluster onto its tertiary structure derived from cryo-EM data. Some footprints flank the first triplet to be translated in tmRNA, suggesting that SmpB participates in the insertion of the tmRNA-encoded reading frame into the decoding center. To discriminate between a conformational rearrangement of tmRNA and independent binding sites, surface plasmon resonance was used and has identified three independent binding sites of SmpB on the RNA, including the site on the tRNA domain. Accordingly, SmpB is proposed to move on the tmRNA scaffold during trans-translation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.