Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain

RNA

Volumn 5, Issue 11, 1999, Pages 1399-1407

  Basu, Soumitra ^a   Strobel, Scott A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Group I intron; Metal binding; RNA folding

Indexed keywords

2' DEOXYNUCLEOSIDE; MANGANESE; PHOSPHOROTHIOIC ACID; RNA;

ARTICLE; BINDING SITE; CATALYSIS; CRYSTAL STRUCTURE; INTRON; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; TETRAHYMENA;

ANIMALS; CATIONS, DIVALENT; CRYSTALLOGRAPHY, X-RAY; DNA, PROTOZOAN; INTRONS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PLASMIDS; RNA, CATALYTIC; RNA, PROTOZOAN; TETRAHYMENA; THIONUCLEOTIDES;

TETRAHYMENA;

EID: 0032707136     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S135583829999115X     Document Type: Article

References (43)

1. Basu S, Rambo RP, Strauss-Soukup J, Cate JH, Ferré-D'Amaré AR, Strobel SA, Doudna JA. 1998. A specific monovalent metal ion integral to the A-A platform of the RNA tetraloop receptor. Nat Struct Biol 5:986-992.
2. Bond MD, Holmquist B, Vallee BL. 1986. Thioamide substrate probes of metal-substrate interactions in carboxypeptidase A catalysis. J Inorg Biochem 28:97-105.
3. Brautigam CA, Steitz TA. 1998. Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. J Mol Biol 277:363-377.
4. Cate JH, Doudna JA. 1996. Metal-binding sites in the major groove of a large ribozyme domain. Structure 4:1221-1229.
5. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA. 1996a. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273:1678-1685.
6. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna JA. 1996b. RNA tertiary structure mediation by adenosine platforms. Science 273:1696-1699.
7. Cate JH, Hanna RL, Doudna JA. 1997. A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol 4:553-558.
8. Celander DW, Cech TR. 1991. Visualizing the higher order folding of a catalytic RNA molecule. Science 251:401-407.
9. Chanfreau G, Jacquier A. 1994. Catalytic site components common to both splicing steps of a group II intron. Science 266:1383-1387.
10. Christian EL, Yarus M. 1992. Analysis of the role of phosphate oxygens in the group I intron from Tetrahymena. J Mol Biol 228:743-758.
11. Christian EL, Yarus M. 1993. Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena. Biochemistry 32:4475-4480.
12. Cotton FA, Wilkinson G. 1988. Advances in inorganic chemistry, 5th ed. New York: Wiley.
13. Dahm SC, Uhlenbeck OC. 1991. Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30:9464-9469.
14. Doherty EA, Doudna JA. 1997. The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry 36:3159-3169.
15. 3+ bound to tRNA. Biophys Chem 21:91-101.
16. Eckstein F. 1985. Nucleoside phosphorothioates. Ann Rev Biochem 54:367-402.
17. Gesteland RF, Cech TR, Atkins JF. 1999. The RNA world, 2nd ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
18. Gish G, Eckstein F. 1988. DNA and RNA sequence determination based on phosphorothioate chemistry. Science 240:1520-1522.
19. P-phosphorothioate modifications in RNase P RNA that interfere with tRNA binding. EMBO J 14:2935-2944.
20. Irving H, Williams RJP. 1953. The stability of transition metal complexes. J Chem Soc 3:3192-3210.
21. Jack A, Ladner JE, Rhodes D, Brown RS, Klug A. 1977. A crystallographic study of metal-binding to yeast phenylalanine transfer RNA. J Mol Biol 111:315-328.
22. Knoll R, Bald R, Furste JP. 1997. Complete identification of nonbridging phosphate oxygens involved in hammerhead cleavage. RNA 3:132-140.
23. Murphy FL, Cech TR. 1993. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry 32:5291-5300.
24. Murphy FL, Cech TR. 1994. GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain. J Mol Biol 236:49-63.
25. Murphy FL, Wang Y-H, Griffith JD, Cech TR. 1994. Coaxially stacked RNA helices in the catalytic center of the Tetrahymena ribozyme. Science 265:1709-1712.
26. Ortoleva-Donnelly L, Szewczak AA, Gutell RR, Strobel SA. 1998. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA 4:498-519.
27. 2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of MgATP and MgADP. Biochemistry 23:5262-5271.
28. Peracchi A, Beigelman L, Scott EC, Uhlenbeck OC, Herschlag D. 1997. Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation. J Biol Chem 272:26822-26826.
29. Piccirilli JA, Vyle JS, Caruthers MH, Cech TR. 1993. Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature 362: 85-88.
30. Pley HW, Flaherty KM, McKay DB. 1994. Three-dimensional structure of a hammerhead ribozyme. Nature 372:68-74.
31. Pyle AM. 1993. Ribozymes: A distinct class of metalloenzymes. Science 261:709-714.
32. Rubin JR, Sundaralingam M. 1983. Lead ion binding and RNA chain hydrolysis in phenylalanine tRNA. J Biomol Struct Dyn 1:639-646.
33. Rubin JR, Wang J, Sundaralingam M. 1983. X-ray diffraction study of the zinc(II) binding sites in yeast phenylalanine transfer RNA. Preferential binding of zinc to guanines in purine-purine sequences. Biochim Biophys Acta 756:111-118.
34. Ruffner DE, Uhlenbeck OC. 1990. Thiophosphate interference experiments locate phosphates important for the hammerhead RNA self-cleavage reaction. Nucleic Acids Res 18:6025-6029.
35. Sclavi B, Sullivan M, Chance MR, Brenowitz M, Woodson SA. 1998. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279:1940-1943.
36. Scott WG, Murray JB, Arnold JRP, Stoddard BL, Klug A. 1996. Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme. Science 274:2065-2069.
37. Silverman SK, Cech TR. 1999. Energetics and cooperativity of tertiary hydrogen bonds in RNA structure. Biochemistry 38:8691-8702.
38. Sood VD, Beattie TL, Collins RA. 1998. Identification of phosphate groups involved in metal binding and tertiary interactions in the core of the Neurospora VS ribozyme. J Mol Biol 282:741-750.
39. Sousa R, Padilla R. 1995. A mutant T7 RNA polymerase as a DNA polymerase. EMBO J 14:4609-4621.
40. Szewczak AA, Cech TR. 1997. An RNA internal loop acts as a hinge to facilitate ribozyme folding and catalysis. RNA 3:838-849.
41. Szewczak AA, Podell ER, Bevilacqua PC, Cech TR. 1998. Thermodynamic stability of the P4-P6 domain RNA tertiary structure measured by temperature gradient gel electrophoresis. Biochemistry 37:11162-11170.
42. P-phosphorothioate modification in the precursor tRNA at the RNase P cleavage site. Proc Natl Acad Sci USA 93:8924-8928.
43. Weinstein LB, Jones BCNM, Cosstick R, Cech TR. 1997. A second catalytic metal ion in a group I ribozyme. Nature 388:805-808.