Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent

Journal of Molecular Biology

Volumn 258, Issue 4, 1996, Pages 600-613

  Westhof, Eric ^a   Wesolowski, Donna ^b   Altman, Sidney ^b  

^a CNRS   (France)

^b YALE UNIVERSITY   (United States)

Author keywords

C5 protein; Computer modeling; M1 RNA; Precursor tRNA; RNase P

Indexed keywords

BACTERIAL ENZYME; BACTERIAL RNA; EDETATE IRON; RIBONUCLEASE P; RIBOSE; RIBOZYME; RNA BINDING PROTEIN; RNA PRECURSOR; TRANSFER RNA;

ARTICLE; COMPLEX FORMATION; ENZYME SUBSTRATE COMPLEX; ENZYME SUBUNIT; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN RNA BINDING; RNA CONFORMATION;

EID: 0029866752     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0272     Document Type: Article

References (38)

1. Altamn, S., Kirsebom, L. & Talbot, S. (1993). Recent studies of RNase P. FASEB J. 7, 7-14.
2. Asp catalyzed by the RNA component of Bacillus subtilis ribonuclease P. Biochemistry, 33, 10294-10304.
3. Brown, J. W. & Pace, N. R. (1992). Ribonuclease P RNA and protein subunits from bacteria. Nucl. Acids Res. 20, 1451-1456.
4. Celander, D. W. & Cech, T. R. (1991). Visualizing the higher folding of a catalytic RNA molecule. Science, 251, 401-407.
5. Ciesiolka, J., Hardt, W-D., Schlegl, J., Erdmann, V. A. & Hartmann, R. K. (1994). Lead-ion-induced cleavage of RNase P RNA Eur. J. Biochem. 219, 49-56.
6. Darr, S. C., Brown, J. W. & Pace, N. R. (1992). The varieties of ribonuclease P. Trends. Biochem. Sci. 17, 178-182.
7. Guerrier-Takada, C. & Altman, S. (1992). Reconstitution of enzymatic activity from fragments of M1 RNA. Proc. Natl Acad. Sci. USA, 89, 1266-1270.
8. Guerrier-Takada, C. & Altman, S. (1993). A physical assay for kinetic analysis of the interactions between M1 RNA and tRNA precursor substrates. Biochemistry, 32, 7152-7161.
9. Guerrier-Takada, C., Lumelsky N. & Altman, S. (1989). Specific interactions in RNA enzyme-substrate complexes. Science, 246, 1578-1584.
10. Haas, E. S., Brown, J. W., Pitulle, C. & Pace, N. R. (1994). Further perspective on the catalytic core and secondary structure of ribonuclease P RNA. Proc. Natl Acad. Sci. USA, 91, 2527-2531.
11. Harris, M. E., Nolan, J. M., Malhotra, A., Brown, J. W., Harvey, S. C. & Pace, N. R. (1994). Use of photoaffinity crosslinking and molecular modeling to analyze the global architecture of ribonuclease P RNA. EMBO J. 13, 3953-3963.
12. Jaeger, L., Westhof, E. & Michel, F. (1993). Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. J. Mol. Biol. 234, 331-346.
13. Jaeger, L., Michel, F. & Westhof, E. (1994). Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol. Biol. 236, 1271-1276.
14. Kazakov, S. & Altman, S. (1991). Site-specific cleavage by metal ion cofactors and inhibitors of M1 RNA, the catalytic subunit of RNase P from Escherichia coli. Proc. Natl Acad. Sci. USA, 88, 9193-9197.
15. Kirsebom, L. A. & Svärd, S. G. (1993). Identification of a region within M1 RNA of Escherichia coli RNase P important for the location of the cleavage site on a wild-type precursor. J. Mol. Biol. 231, 594-604.
16. Kirsebom, L. A. & Svärd, S. G. (1994). Base-pairing between Escherichia coli RNase P RNA and its substrate. EMBO J. 13, 4870-4876.
17. Knap, A., Wesolowski, D. & Altman, S. (1990). Protection from chemical modification of nucleotides in complexes of M1 RNA, the catalytic subunit of RNase P from Escherichia coli, and tRNA precursors. Biochimie, 72, 779-790.
18. Krol, A., Westhof, E., Bach, M., Lührmann, R., Ebel, J. P. & Carbon, P. (1990). Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model. Nucl. Acids Res. 18, 3803-3811.
19. Kufel, J. & Kirsebom, L. A. (1994). Cleavage site selection by M1 RNA, the catalytic subunit of Escherichia coli RNase P, is influenced by pH. J. Mol. Biol. 244, 511-521.
20. Kuwajima, K. (1989). The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure. Proteins: Struct. Funct. Genet. 6, 87-103.
21. Latham, J. A. & Cech, T. R. (1989). Defining the inside and the outside of a catalytic RNA molecule. Science, 245, 276-282.
22. Massire, C., Gaspin, C. & Westhof, E. (1994). DRAWNA: a program for drawing schematic views of nucleic acids. J. Mol. Graph. 12, 201-206.
23. Mattsson, J. G., Svärd, S. G. & Kirsebom, L. A. (1994). Characterization of the Borrelia burgdorferi RNase P RNA gene reveals a novel tertiary interaction. J. Mol. Biol. 241, 1-6.
24. McClain, W. H., Guerrier-Takada, C. & Altman, S. (1987). Model substrates for an RNA enzyme. Science, 238, 527-530.
25. Morales, M. J., Wise, C. A., Hollingsworth, M. J. & Martin, N. C. (1989). Characterization of yeast mitochondrial RNase P: an intact RNA subunit is not essential for activity in vitro. Nucl. Acids Res. 17, 6865-6881.
26. Nolan, J. M., Burke, D. M. & Pace, N. R. (1993). Circularly permuted tRNAs as specific photoaffinity probes of ribonuclease P RNA structure. Science, 261, 762-765.
27. Oh, B.-K. & Pace, N. R. (1994). Interaction of the 3′-end of tRNA with ribonuclease P RNA. Nucl. Acids Res. 22, 4087-4094.
28. Pan, T. (1995). Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry, 34, 902-909.
29. Perreault, J.-P. & Altman, S. (1992). Important 2′-hydroxyl groups in model substrates for M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli. J. Mol. Biol. 226, 399-409.
30. Richmond, T. J. (1984). Solvent accessible surface area and excluded volume in proteins. J. Mol. Biol. 178, 63-89.
31. Schlegl, J., Hardt, W.-D., Erdmann, V. A. & Hartmann, R. K. (1994). Contribution of structural elements to Thermus thermophilus ribonuclease P RNA function. EMBO J. 13, 4863-4869.
32. Svärd, S. G. & Kirsebom, L. A. (1992) Several regions of a tRNA precursor determine the Escherichia coli RNAse P cleavage site. J. Mol. Biol. 227, 1019-1031.
33. Svärd, S. G. & Kirsebom, L. A. (1993). Determinants of Escherichia coli RNase P cleavage site selection: a detailed in vitro and in vivo analysis. Nucl. Acids Res. 21, 427-434.
34. Talbot, S. J. & Altman, S. (1994). Gel retardation analysis of the interaction between C5 protein and M1 RNA in the formation of the ribonuclease P holoenzyme from Escherichia coli. Biochemistry, 33, 1399-1405.
35. Tallsjö, A., Svärd, S. G., Kufel, J. & Kirsebom, L. A. (1993). A novel tertiary interaction in M1 RNA, the catalytic subunit of Escherichia coli RNase P. Nucl. Acids Res. 21, 3927-3933.
36. Vioque, A., Arnez, J. & Altman, S. (1988). Protein-RNA interactions in the RNase P holoenzyme from Escherichia coli. J. Mol. Biol. 202, 835-848.
37. Westhof, E. & Altman, S. (1994). Three-dimensional working model of M1 RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli. Proc. Natl Acad. Sci. USA, 91, 5133-5137.
38. Zito, K., Hüttenhofer, A. & Pace, N. R. (1993). Lead-catalyzed cleavage of ribonuclease P RNA as a probe for integrity of tertiary structure. Nucl. Acids Res. 21, 5916-5920.