Structural studies of the tRNA domain of tmRNA

Scott M. Stagg, Ashley A. Frazer-Abel, Paul J Hagerman, Stephen C. Harvey

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

tmRNA is a small, stable prokaryotic RNA. It rescues ribosomes that have become stalled during the translation of mRNA fragments lacking stop codons, or during periods of tRNA scarcity. It derives its name from the presence of two separate domains, one that functions as a tRNA, and another that serves as an mRNA. We have carried out modeling and transient electric birefringence studies to determine the angle between the acceptor stem and anticodon stem of the tRNA domain of Eschericia coli tmRNA. The results of the modeling studies yielded an interstem angle of 110°, in agreement with the lower end of the range of angles (111°-137°) determined experimentally for various solution conditions. The range of experimental angles is greater than the angles observed for any of the tRNA crystal structures, in line with the presence of a shortened D stem. The secondary structure of the tRNA domain is conserved for all known tmRNA sequences, so we propose that the angle is also conserved. These results also suggest that the region of tmRNA between P2a and P2b may interact with the decoding site of the ribosome.

Original languageEnglish (US)
Pages (from-to)727-735
Number of pages9
JournalJournal of Molecular Biology
Volume309
Issue number3
DOIs
StatePublished - Jun 8 2001

Fingerprint

Transfer RNA
Ribosomes
Birefringence
Anticodon
Terminator Codon
Protein Biosynthesis
Names
tmRNA
RNA
Messenger RNA

Keywords

  • Molecular modeling
  • RNA structure
  • SsrA RNA
  • tmRNA
  • Transient electric birefringence

ASJC Scopus subject areas

  • Virology

Cite this

Structural studies of the tRNA domain of tmRNA. / Stagg, Scott M.; Frazer-Abel, Ashley A.; Hagerman, Paul J; Harvey, Stephen C.

In: Journal of Molecular Biology, Vol. 309, No. 3, 08.06.2001, p. 727-735.

Research output: Contribution to journalArticle

Stagg, Scott M. ; Frazer-Abel, Ashley A. ; Hagerman, Paul J ; Harvey, Stephen C. / Structural studies of the tRNA domain of tmRNA. In: Journal of Molecular Biology. 2001 ; Vol. 309, No. 3. pp. 727-735.
@article{76c54471339c4abbb182efcfc43a53a9,
title = "Structural studies of the tRNA domain of tmRNA",
abstract = "tmRNA is a small, stable prokaryotic RNA. It rescues ribosomes that have become stalled during the translation of mRNA fragments lacking stop codons, or during periods of tRNA scarcity. It derives its name from the presence of two separate domains, one that functions as a tRNA, and another that serves as an mRNA. We have carried out modeling and transient electric birefringence studies to determine the angle between the acceptor stem and anticodon stem of the tRNA domain of Eschericia coli tmRNA. The results of the modeling studies yielded an interstem angle of 110°, in agreement with the lower end of the range of angles (111°-137°) determined experimentally for various solution conditions. The range of experimental angles is greater than the angles observed for any of the tRNA crystal structures, in line with the presence of a shortened D stem. The secondary structure of the tRNA domain is conserved for all known tmRNA sequences, so we propose that the angle is also conserved. These results also suggest that the region of tmRNA between P2a and P2b may interact with the decoding site of the ribosome.",
keywords = "Molecular modeling, RNA structure, SsrA RNA, tmRNA, Transient electric birefringence",
author = "Stagg, {Scott M.} and Frazer-Abel, {Ashley A.} and Hagerman, {Paul J} and Harvey, {Stephen C.}",
year = "2001",
month = "6",
day = "8",
doi = "10.1006/jmbi.2001.4632",
language = "English (US)",
volume = "309",
pages = "727--735",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press Inc.",
number = "3",

}

TY - JOUR

T1 - Structural studies of the tRNA domain of tmRNA

AU - Stagg, Scott M.

AU - Frazer-Abel, Ashley A.

AU - Hagerman, Paul J

AU - Harvey, Stephen C.

PY - 2001/6/8

Y1 - 2001/6/8

N2 - tmRNA is a small, stable prokaryotic RNA. It rescues ribosomes that have become stalled during the translation of mRNA fragments lacking stop codons, or during periods of tRNA scarcity. It derives its name from the presence of two separate domains, one that functions as a tRNA, and another that serves as an mRNA. We have carried out modeling and transient electric birefringence studies to determine the angle between the acceptor stem and anticodon stem of the tRNA domain of Eschericia coli tmRNA. The results of the modeling studies yielded an interstem angle of 110°, in agreement with the lower end of the range of angles (111°-137°) determined experimentally for various solution conditions. The range of experimental angles is greater than the angles observed for any of the tRNA crystal structures, in line with the presence of a shortened D stem. The secondary structure of the tRNA domain is conserved for all known tmRNA sequences, so we propose that the angle is also conserved. These results also suggest that the region of tmRNA between P2a and P2b may interact with the decoding site of the ribosome.

AB - tmRNA is a small, stable prokaryotic RNA. It rescues ribosomes that have become stalled during the translation of mRNA fragments lacking stop codons, or during periods of tRNA scarcity. It derives its name from the presence of two separate domains, one that functions as a tRNA, and another that serves as an mRNA. We have carried out modeling and transient electric birefringence studies to determine the angle between the acceptor stem and anticodon stem of the tRNA domain of Eschericia coli tmRNA. The results of the modeling studies yielded an interstem angle of 110°, in agreement with the lower end of the range of angles (111°-137°) determined experimentally for various solution conditions. The range of experimental angles is greater than the angles observed for any of the tRNA crystal structures, in line with the presence of a shortened D stem. The secondary structure of the tRNA domain is conserved for all known tmRNA sequences, so we propose that the angle is also conserved. These results also suggest that the region of tmRNA between P2a and P2b may interact with the decoding site of the ribosome.

KW - Molecular modeling

KW - RNA structure

KW - SsrA RNA

KW - tmRNA

KW - Transient electric birefringence

UR - http://www.scopus.com/inward/record.url?scp=0035827219&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0035827219&partnerID=8YFLogxK

U2 - 10.1006/jmbi.2001.4632

DO - 10.1006/jmbi.2001.4632

M3 - Article

C2 - 11397092

AN - SCOPUS:0035827219

VL - 309

SP - 727

EP - 735

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 3

ER -