Structure and stability of variants of the sarcin-ricin loop of 28S rRNA: NMR studies of the prokaryotic SRL and a functional mutant

RNA

Volumn 4, Issue 10, 1998, Pages 1203-1215

  Seggerson, Kathy ^a   Moore, Peter B ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

23S rRNA; Alpha sarcin; Bulged G; Ricin; Structure

Indexed keywords

RICIN; RNA 28S;

ARTICLE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROKARYOTE; RIBOSOME; RNA CONFORMATION; RNA STRUCTURE;

ADENOSINE; ANIMALS; ENDORIBONUCLEASES; ESCHERICHIA COLI; FUNGAL PROTEINS; HYDROGEN-ION CONCENTRATION; MUTATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; RATS; RICIN; RNA, RIBOSOMAL, 28S; TEMPERATURE;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 0031668475     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838298980773     Document Type: Article

References (31)

1. Benevides JM, Thomas GJ Jr. 1985. Dependence of purine 8C-H exchange on nucleic acid conformation and base-pairing geometry: A dynamic probe of DNA and RNA secondary structures. Biopolymers 24:667-682.
2. Brandes R, Ehrenberg A. 1986. Kinetics of the proton-deuteron exchange at position H8 of adenine and guanine in DNA. Nucleic Acids Res 14:9491-9508.
3. Correll CC, Freeborn B, Moore PB, Steitz TA. 1997. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 91:705-712.
4. Dallas A, Moore PB. 1997. The loop E-loop D region of Escherichia coli 5S rRNA: The solution structure reveals an unusual loop that may be important for binding ribosomal proteins. Structure 5:1639-1653.
5. Draper DE, Gluick TC. 1995. Melting studies of RNA unfolding and RNA-ligand interactions. Methods Enzymol 259:281-305.
6. Endo Y, Tsurugi K. 1988. The RNA N-glycosidase activity of ricin A-chain. J Biol Chem 263:8735-8739.
7. Endo Y, Wool IG. 1982. The site of action of α-sarcin on eukaryotic ribosomes. J Biol Chem 257:9054-9060.
8. Farber NM, Cantor CR. 1981. A slow tritium exchange study of the solution structure of Escherichia coli 5S ribosomal RNA. J Mol Biol 146:223-239.
9. Fernandez-Puentes C, Vazquez D. 1977. Effects of some proteins that inactivate eukaryotic ribosomes. FEBS Lett 78:143-146.
10. Gamble RC, Schoemaker HJP, Jekowsky E, Schimmel PR. 1976. Rate of tritium labeling of specific purines in relation to nucleic acid and particularly transfer RNA conformation. Biochemistry 13:2791-2799.
11. Gluck A, Endo Y, Wool IG. 1992. Ribosomal RNA identity elements for ricin A-chain recognition and catalysis. Analysis with tetraloop mutants. J Mol Biol 226:411-424.
12. Gluck A, Wool IG. 1996. Determination of the 28S ribosomal RNA identity element (G4319) for alpha-sarcin and the relationship of recognition to the selection of the catalytic site. J Mol Biol 256:838-848.
13. Heus HA, Pardi A. 1991. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253:191-194.
14. Lane MJ, Thomas GJ Jr. 1979. Kinetics of hydrogen-deuterium exchange in guanosine 5′-monophosphate and guanosine 3′:5′-monophosphate determined by laser-Raman spectroscopy. Biochemistry 18:3839-3846.
15. Liu R, Liebman SW. 1996. A translational fidelity mutation in the universally conserved sarcin/ricin domain of 25S yeast ribosomal RNA. RNA 2:254-263.
16. Marchant A, Hartley MR. 1994. Mutational studies on the α-sarcin loop of Escherichia coli 23S ribosomal RNA. Eur J Biochem 226:141-147.
17. 13C-labeled RNA. J Am Chem Soc 119:7361-7366.
18. Marky LA, Breslauer KJ. 1987. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 26:1601-1620.
19. Munishkin A, Wool IG. 1997. The ribosome-in-pieces: Binding of elongation factor EF-G to oligoribonucleotides that mimic the sarcin/ ricin and thiostrepton domains of 23S ribosomal RNA. Proc Natl Acad Sci USA 94:12280-12284.
20. Nierhaus KH, Schilling-Bartetzko S, Twardowski T. 1992. The two main states of the elongating ribosome and the role of the α-sarcin stem-loop structure of 23S RNA. Biochimie 74:403-410.
21. O'Connor M, Dahlberg AE. 1996. The influence of base identity and base pairing on the function of the α-sarcin loop of 23S rRNA. Nucleic Acids Res 24:2701-2705.
22. Saenger W. 1984. Principles of nucleic acid structure. New York: Springer-Verlag.
23. Schoemaker HJP, Gamble RC, Budzik GP, Schimmel PR. 1976. Comparison of isotope labeling patterns of purines in three specific transfer RNAs. Biochemistry 15:2800-2803.
24. Stallings SC, Moore PB. 1997. The structure of an essential splicing element: Stem loop IIa from yeast U2 snRNA. Structure 5:1173-1185.
25. Stein EG, Rice LM, Brunger AT. 1997. Torsion angle molecular dynamics: A new, efficient tool for NMR structure calculation. J Magn Reson B 127:154-157.
26. Szewczak AA, Moore PB. 1995. The sarcin/ricin loop, a modular RNA. J Mol Biol 247:81-98.
27. Szewczak AA, Moore PB, Chan YL, Wool IG. 1993. The conformation of the sarcin/ricin loop from 28S ribosomal RNA. Proc Natl Acad Sci USA 90:9581-9585.
28. Tapprich WE, Dahlberg AE. 1990. A single base mutation at position 2661 in E. coli 23S ribosomal RNA affects the binding of ternary complex to the ribosome. EMBO J 9:2649-2655.
29. Tomasz M, Olson J, Mercado CM. 1972. Mechanism of the isotopic exchange of the C-8 hydrogen of purines in nucleosides and in deoxyribonucleic acid. Biochemistry 11:1235-1241.
30. Wimberly B, Varani G, Tinoco I Jr. 1993. The conformation of loop E of eukaryotic 5S ribosomal RNA. Biochemistry 32:1078-1087.
31. Wool IG, Gluck A, Endo Y. 1992. Ribotoxin recognition of ribosomal RNA and a proposal for the mechanism of translocation. Trends Biochem Sci 17:266-269.