Outersphere and innersphere coordinated metal ions in an aminoacyl-tRNA synthetase ribozyme

Nucleic Acids Research

Volumn 30, Issue 23, 2002, Pages 5151-5159

  Saito, Hirohide ^a,b,c   Suga, Hiroaki ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b UNIVERSITY OF TOKYO   (Japan)

^c CANCER INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; AMMONIA; COBALT COMPLEX; MAGNESIUM ION; METAL ION; PHENYLALANINE; RIBOZYME; TERBIUM; TRANSFER RNA; WATER;

AMINOACYLATION; BINDING AFFINITY; BINDING SITE; CATALYST; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; COVALENT BOND; GENE MAPPING; IN VITRO STUDY; METAL BINDING; PRIORITY JOURNAL; REVIEW;

AMINO ACYL-TRNA SYNTHETASES; BASE SEQUENCE; BINDING SITES; BINDING, COMPETITIVE; CATALYSIS; CATIONS; DOSE-RESPONSE RELATIONSHIP, DRUG; KINETICS; MAGNESIUM; METALS; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; MUTATION; NUCLEIC ACID CONFORMATION; PHENYLALANINE; RNA PRECURSORS; RNA, CATALYTIC; RNA, TRANSFER; TERBIUM;

EID: 0036930398     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf641     Document Type: Review

References (33)

1. Feig,A.L. and Uhlenbeck,O.C. (1999) The role of metal ions in RNA biochemistry. In Atkins,J.F. (ed.), The RNA World, 2nd Edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 287-319.
2. Takagi,Y., Warashina,M., Stec,W.J., Yoshinari,K. and Taira,K. (2001) Recent advances in the elucidation of the mechanisms of action of ribozymes. Nucleic Acids Res., 29, 1815-1834.
3. Fedor,M.J. (2002) The role of metal ions in RNA catalysis. Curr. Opin. Struct. Biol., 12, 289-295.
4. Hanna,R. and Doudna,J.A. (2000) Metal ions in ribozyme folding and catalysis. Curr. Opin. Chem. Biol., 4, 166-170.
5. Dahm,A.C. and Uhlenbeck,O.C. (1991) Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry, 30, 9464-9469.
6. Dahm,A.C., Derrick,W.B. and Uhlenbeck,O.C. (1993) Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism. Biochemistry, 32, 13040-13045.
7. Scott,W.G., Murray,J.B., Arnold,J.R.P., Stoddard,B.L. and Klug,A. (1996) Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science, 274, 2065-2069.
8. Murray,J.B., Seyhan,A.A., Walter,N.G., Burke,J.M. and Scott,W.G. (1998) The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol., 5, 587-595.
9. Curtis,E.A. and Bartel,D.P. (2001) The hammerhead cleavage reaction in monovalent cations. RNA, 7, 546-552.
10. O'Rear,J.L., Wang,S., Feig,A.L., Beigelman,L., Uhlenbeck,O.C. and Herschlag,D. (2001) Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. RNA, 7, 537-545.
11. Walter,N.G. and Burke,J.M. (1998) The hairpin ribozyme: structure, assembly and catalysis. Curr. Opin. Chem. Biol., 2, 24-30.
12. Young,K.J., Gill,F. and Grasby,J.A. (1997) Metal ions play a passive role in the hairpin ribozyme catalysed reaction. Nucleic Acids Res., 25, 3760-3766.
13. Rupert,P.B. and Ferre-D'Amare,A.R. (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature, 410, 780-786.
14. Wilson,T.J. and Lilley,D.M. (2002) Metal ion binding and the folding of the hairpin ribozyme. RNA, 8, 587-600.
15. Saito,H., Kourouklis,D. and Suga,H. (2001) An in vitro evolved precursor tRNA with aminoacylation activity. EMBO J., 20, 1797-1806.
16. Saito,H., Watanabe,K. and Suga,H. (2001) Concurrent molecular recognition of the amino acid and tRNA by a ribozyme. RNA, 7, 1867-1878.
17. Suga,H., Cowan,J.A. and Szostak,J.W. (1998) Unusual metal ion catalysis in an acyl-transferase ribozyme. Biochemistry, 37, 10118-10125.
18. Hampel,A. and Cowan,J.A. (1997) A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage. Curr. Biol., 4, 513-517.
19. Nesbitt,S., Hegg,L.A. and Fedor,M.J. (1997) An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis. Chem. Biol., 4, 619-630.
20. Horton,T.E. and DeRose,V.J. (2000) Cobalt hexammine inhibition of the hammerhead ribozyme. Biochemistry, 39, 11408-11416.
21. Lee,N. and Suga,H. (2001) Essential roles of innersphere metal ions for the formation of the glutamine binding site in a bifunctional ribozyme. Biochemistry, 40, 13633-13643.
22. Vaidya,A. and Suga,H. (2001) Diverse roles of metal ions in acyltransferase ribozymes. Biochemistry, 40, 7200-7210.
23. Feig,A.L., Scott,W.G. and Uhlenbeck,O.C. (1998) Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb(III). Science, 279, 81-84.
24. Feig,A.L., Panek,M., Horrocks,W.D.J. and Uhlenbeck,O.C. (1999) Probing the binding of Tb(III) and Eu(III) to the hammerhead ribozyme using luminescence spectroscopy. Chem. Biol., 6, 801-810.
25. Hargittai,M.R. and Musier-Forsyth,K. (2000) Use of terbium as a probe of tRNA tertiary structure and folding. RNA, 6, 1672-1680.
26. Walter,N.G., Yang,N. and Burke,J.M. (2000) Probing non-selective cation binding in the hairpin ribozyme with Tb(III). J. Mol. Biol., 298, 539-555.
27. Sigel,R.K., Vaidya,A. and Pyle,A.M. (2000) Metal ion binding sites in a group II intron core. Nature Struct. Biol., 7, 1111-1116.
28. Flynn-Charlebois,A., Lee,N. and Suga,H. (2001) A single metal ion plays structural and chemical roles in an aminoacyl-transferase ribozyme. Biochemistry, 40, 13623-13632.
29. Zhou,J.M., Zhou,D.M., Takagi,Y., Kasai,Y., Inoue,A., Baba,T. and Taira,K. (2002) Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme. Nucleic Acids Res., 30, 2374-2382.
30. Nakano,S., Procter,D.J. and Bevilacqua,P.C. (2001) Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism. Biochemistry, 40, 12022-12038.
31. Cate,J.H. and Doudna,J.A. (1996) Metal-binding sites in the major groove of a large ribozyme domain. Structure, 4, 1221-1229.
32. Kieft,J.S. and Tinoco,J.I. (1997) Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt(III) hexammine. Structure, 5, 713-721.
33. Sprinzl,M., Horn,C., Brown,M., Ioudovitch,A. and Steinberg,S. (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res., 26, 148-153.