Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy

Nucleic Acids Research

Volumn 32, Issue 21, 2004, Pages 6358-6366

  Schmitz, Michael ^a,b  

^a HEINRICH HEINE UNIVERSITY   (Germany)

^b FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; COBALT; CYSTEINE; MAGNESIUM DERIVATIVE; METAL ION; PROTON; RIBONUCLEASE P; RNA; URIDINE;

ANIMAL CELL; ARTICLE; BASE PAIRING; BINDING KINETICS; BINDING SITE; CONTROLLED STUDY; CORRELATION ANALYSIS; ESCHERICHIA COLI; GENE MUTATION; GENETIC VARIABILITY; MOLECULAR PROBE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN FUNCTION; RNA BINDING; RNA CONFORMATION; RNA STRUCTURE; STRUCTURE ANALYSIS; THERMOTOGA MARITIMA; WILD TYPE;

BASE SEQUENCE; BINDING SITES; CATIONS, DIVALENT; COBALT; ESCHERICHIA COLI; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; POINT MUTATION; PROTONS; RIBONUCLEASE P;

EID: 13444254309     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh961     Document Type: Article

References (39)

1. Pace,N.R. and Brown,J.W. (1995) Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J. Bacteriol., 177, 1919-1928.
2. Harris,M.E., Frank,D.N. and Pace,N.R. (1998) Structure and catalytic function of the bacterial ribonuclease P enzyme. In Simons, R.W. and Grunberg-Manago, M., (eds), RNA Structure and Function. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 309-337.
3. Guerrier-Takada,C., Gardiner,K., Marsh,T., Pace,N.R. and Altman,S. (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35, 849-857.
4. Guerrier-Takada,C., Haydock,K., Allen,L. and Altman,S. (1986) Metal ion requirements and other aspects of the reaction catalyzed by M1 RNA, the RNA subunit of ribonuclease P from Escherichia coli. Biochemistry, 25, 1509-1515.
5. Kurz,J.C. and Fierke,C.A. (2002) The affinity of magnesium binding sites in the Bacillus subtilis RNase P·pre-tRNA complex is enhanced by the protein subunit. Biochemistry, 41, 9545-9558,
6. Harris,M.E., Nolan,J.M., Malhotra,A., Brown,J.W., Harvey,S. and 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.
7. Massire,C., Jaeger,L. and Westhof.E. (1998) Derivation of the three dimensional architecture of bacterial ribonuclease P RNA from comparative sequence analysis. J. Mol. Biol., 279, 773-793.
8. Chen,J.L., Nolan,J.M., Harris,M.E. and Pace,N.R. (1998) Comparative photocross-linking analysis of the tertiary structures of Escherichia coli and Bacillus subtilis RNase P RNAs. EMBO J. 17, 1515-1525.
9. Krasilnikov,A.S., Jang,X., Pan,T. and Mondragon,A. (2003) Crystal structure of the specificity domain of ribonuclease P. Nature 42, 760-764.
10. Kanzatsev,A.V., Krivenko,A.A., Harrington,D.J., Carter,R.J., Holbrook,S.R., Adams,P.D. and Pace,N.R. (2003) High-resolution structure of RNase P protein from Thermotoga maritima. Proc. Natl Acad. Sci. USA 100, 7497-7502.
11. Tsai,H.-Y., Masquida,B., Biswas,R., Westhof,E. and Gopalan,V. (2003) Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme. J. Mol. Biol., 325, 661-675.
12. Kanzatsev,A.V. and Pace,N.R. (1998) Identification by modification-interference of purine N-7 and ribose 2′-OH groups critical for catalysis by bacterial ribonuclease P. RNA, 4, 937-947.
13. Hardt,W.-D., Erdmann,V.A. and Hartmann,R.K. (1996) Rp-deoxy-phosphorothioate modification interference experiments identify 2′-OH groups in RNase P RNA that are crucial to tRNA binding. RNA 2, 1189-1198.
14. Christian,E.L., Kaye,N.M. and Harris,M.E. (2002) Evidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA. EMBO J., 21, 2253-2262.
15. Harris,M.E. and Pace,N.R. (1995) Identification of phosphates involved in catalysis by the ribozyme RNase P RNA. RNA, 1, 210-218.
16. Frank,D.N., Ellington,A.D. and Pace,N.R. (1996) In vitro selection of RNase P RNA reveals optimized catalytic activity in highly conserved structural domain. RNA, 2, 1179-1188.
17. Frank,D.N. and Pace,N.R. (1997) In vitro selection for altered divalent metal specificity in the RNase P RNA. Proc. Natl Acad. Sci. USA, 94, 14255-14360.
18. Schmitz,M. and Tinoco,I.,Jr (2000) Solution structure and metal-ion binding of the P4 element from bacterial Rnase P RNA. RNA 6, 1212-1225.
19. Kaye,N.M., Zahler,N.H., Christian,E.L. and Harris,M.E. (2002) Conservation of helical structure contributes to functional metal ion interactions in the catalytic domain of ribonuclease P RNA. J. Mol. Biol., 324, 429-442.
20. 2+(aq) binding sites. J. Inorg. Biochem., 49 171-175.
21. Kieft,J.S. and Tinoco,I.,Jr (1997) Solution structure of a metal binding site in the major groove of RNA complexed with cobalt (III) hexammine. Structure, 5, 713-721.
22. Colmenarejo,G. and Tinoco,I.,Jr (1999) Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme. J. Mol. Biol., 290, 119-135.
23. Rüdisser,S. and Tinoco,I.,Jr (2000) Structure and thermodynamics. of metal-ion binding to GA mismatches and to the GAAA tetraloop. J. Mol. Biol., 295, 1211-1223.
24. Wyatt,J.R., Chastain,M. and Puglisi,J.D. (1991) Synthesis and purification of large amounts of RNA oligonucleotides. Biotechniques 11, 764-769.
25. Sklenár,V. and Bax,A. (1987) Spin-echo water suppression for the generation of pure-phase two-dimensional NMR spectra. J. Magn. Reson., 74, 469-479.
26. Macura,S., Wüthrich,K. and Ernst,R.R. (1982) Separation and suppression of coherent transfer effects in two-dimensional NOE and chemical exchange spectroscopy. J. Magn. Reson., 46, 269-282.
27. Shaka,A.J. and Freeman,R. (1983) Simplification of NMR spectra by filtration through multiple-quantum coherence. J. Magn. Reson., 51, 169-173.
28. Müller,N., Ernst,R.R. and Wüthrich,K. (1986) Multiple-quantum-filtered two-dimensional correlated NMR spectroscopy of proteins. J. Am. Chem. Soc., 108, 6482-6492.
29. Shaka,A.J., Barker,P.B. and Freeman,R. (1985) Computer-optimized decoupling scheme for wideband applications and low-level operation. J. Magn. Reson., 64, 547-522.
30. Kellogg,G.W. (1992) Proton-detected hetero-TOCSY experiments with application to nucleic acids. J. Magn. Reson., 98, 176-182.
31. 31P-driven NMR procedures for complete assignment of backbone resonances in oligodeoxyribonucleotides. J. Biomol. NMR, 3, 577-595.
32. 31P resonances with anomeric and aromatic 1H resonances in RNA. J. Am. Chem. Soc., 114, 2727-2728.
33. Rucker,S.P. and Shaka,A.J. (1989) Broadband homonuclear cross polarization in 2D N.M.R. using DIPSI-2. Mol. Phys., 68, 509-517.
34. Cheong,C., Varani,G. and Tinoco,I.,Jr (1990) Solution structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC. Nature, 346, 680-682.
35. Brünger, A.T. (1993) X-PLOR Version 3.1: A System for X-ray Crystallography and NMR, Yale University Press, New Haven, CT, USA.
36. Wimberly,B., Varani,G. and Tinoco,I.,Jr (1993) The conformation of loop E of eukaryotic 5S ribosomal RNA. Biochemistry 32, 1078-1087.
37. Varani,G., Aboul-ela,F. and Allain,F.H.-T. (1996) NMR investigation of RNA structure. Progr. Nucl. Magn. Reson. Spectrosc. 29, 51-127.
38. Varani,G. and Tinoco,I.,Jr (1991) RNA structure and NMR spectroscopy. Quart. Revs. Biophysics, 24, 479-532.
39. Allain,F.H.T and Varani,G. (1995) Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns. Nucleic Acids Res., 23, 341-350.