Crystal structure of the RNA component of bacterial ribonuclease P

Nature

Volumn 437, Issue 7058, 2005, Pages 584-587

  Torres Larios, Alfredo ^a   Swinger, Kerren K ^a   Krasilnikov, Andrey S ^a,c   Pan, Tao ^b   Mondragón, Alfonso ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; ENZYMES; MICROORGANISMS; MOLECULAR STRUCTURE; RNA;

INTRA-DOMAIN INTERACTIONS; PRECURSOR MOLECULES; RIBONUCLEASE;

CRYSTAL STRUCTURE;

BACTERIAL ENZYME; BACTERIAL RNA; RIBONUCLEASE P; TRANSFER RNA;

BIOLOGY;

ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME LOCALIZATION; ENZYME STRUCTURE; MOLECULE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; THERMOTOGA MARITIMA; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ENZYME ACTIVE SITE; ENZYMOLOGY; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS); THERMOTOGA MARITIMA;

CATALYTIC DOMAIN; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RIBONUCLEASE P; RNA, BACTERIAL; RNA, TRANSFER; THERMOTOGA MARITIMA;

EID: 25644433566     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature04074     Document Type: Article

References (30)

1. Guerrier-Takada, C., Gardiner, K., Marsh., T., Pace, N. & Altman, S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849-857 (1983).
2. Christian, E. L., Zahler, N. H., Kaye, N. M. & Harris, M. E. Analysis of substrate recognition by the ribonucleoprotein endonuclease RNase P. Methods 28, 307-322 (2002).
3. McClain, W. H., Guerrier-Takada, C. & Altman, S. Model substrates for an RNA enzyme. Science 238, 527-530 (1987).
4. Kirsebom, L. A. & Svard, S. G. Base pairing between Escherichia coli RNase P RNA and its substrate. EMBO J. 13, 4870-4876 (1994).
5. Christian, E. L., Kaye, N. M. & Harris, M. E. Evidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA. EMBO J. 21, 2253-2262 (2002).
6. Beebe, J. A., Kurz, J. C. & Fierke, C. A. Magnesium ions are required by Bacillus subtilis ribonuclease P RNA for both binding and cleaving precursor tRNAAsp. Biochemistry 35, 10493-10505 (1996).
7. Perreault, J. P. & Altman, S. Pathway of activation by magnesium ions of substrates for the catalytic subunit of RNase P from Escherichia coli. J. Mol. Biol. 230, 750-756 (1993).
8. Smith, D. & Pace, N. R. Multiple magnesium ions in the ribonuclease P reaction mechanism. Biochemistry 32, 5273-5281 (1993).
9. Kurz, J. C. & Fierke, C. A. Ribonuclease P: a ribonucleoprotein enzyme. Curr. Opin. Chem. Biol. 4, 553-558 (2000).
10. Pannucci, J. A., Haas, E. S., Hall, T. A., Harris, J. K. & Brown, J. W. RNase P RNAs from some Archaea are catalytically active. Proc. Natl Acad. Sci. USA 96, 7803-7808 (1999).
11. Reich, C., Olsen, G. J., Pace, B. & Pace, N. R. Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme. Science 239, 178-181 (1988).
12. Loria, A. & Pan, T. Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 2, 551-563 (1996).
13. Krasilnikov, A. S., Yang, X., Pan, T. & Mondragon, A. Crystal structure of the specificity domain of ribonuclease P. Nature 421, 760-764 (2003).
14. Krasilnikov, A. S., Xiao, Y., Pan, T. & Mondragon, A. Basis for structural diversity in homologous RNAs. Science 306, 104-107 (2004).
15. Chen, J.-L. & Pace, N. R. Identification of the universally conserved core of ribonuclease P RNA. RNA 3, 557-560 (1997).
16. Massire, C., Jaeger, L. & Westhof, E. Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J. Mol. Biol. 279, 773-793 (1998).
17. Harris, M. E. et al. Use of photoaffinity crosslinking and molecular modeling to analyse the global architecture of ribonuclease P RNA. EMBO J. 13, 3953-3963 (1994).
18. Guerrier-Takada, C. & Altman, S. Reconstitution of enzymatic activity from fragments of M1 RNA. Proc. Natl Acad. Sci. USA 89, 1266-1270 (1992).
19. Harris, M. E., Kazantsev, A. V., Chen, J. L. & Pace, N. R. Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking. RNA 3, 561-576 (1997).
20. Brown, J. W. et al. Comparative analysis of ribonuclease P RNA using gene sequences from natural microbial populations reveals tertiary structural elements. Proc. Natl Acad. Sci. USA 93, 3001-3006 (1996).
21. Massire, C., Jaeger, L. & Westhof, E. Phylogenetic evidence for a new tertiary interaction in bacterial RNase P RNAs. RNA 3, 553-556 (1997).
22. Siegel, R. W., Banta, A. B., Haas, E. S., Brown, J. W. & Pace, N. R. Mycoplasma fermentans simplifies our view of the catalytic core of ribonuclease P RNA. RNA 2, 452-462 (1996).
23. LaGrandeur, T. E., Huttenhofer, A., Noller, H. F. & Pace, N. R. Phylogenetic comparative chemical footprint analysis of the interaction between ribonuclease P RNA and tRNA. EMBO J. 13, 3945-3952 (1994).
24. Odell, L., Huang, V., Jakacka, M. & Pan, T. Interaction of structural modules in substrate binding by the ribozyme from Bacillus subtilis RNase P. Nucleic Acids Res. 26, 3717-3723 (1998).
25. Loria, A. & Pan, T. Recognition of the T stem-loop of a pre-tRNA substrate by the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry 36, 6317-6325 (1997).
26. Zahler, N. H., Christian, E. L. & Harris, M. E. Recognition of the 5′ leader of pre-tRNA substrates by the active site of ribonuclease P. RNA 9, 734-745 (2003).
27. Tsai, H. Y., Masquida, B., Biswas, R., Westhof, E. & Gopalan, V. Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme. J. Mol. Biol. 325, 661-675 (2003).
28. delaFortelle, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472-494 (1997).
29. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240-255 (1997).
30. Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).