Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis

RNA

Volumn 8, Issue 7, 2002, Pages 861-872

  Shan, Shu Ou ^a   Herschlag, Daniel ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Conformational change; Mechanistic analysis; Metal ion; Ribozyme; RNA catalysis

Indexed keywords

GUANOSINE; METAL ION; OLIGONUCLEOTIDE; RIBOZYME; RNA;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; ENERGY TRANSFER; MODEL; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ASSAY; RNA ANALYSIS; RNA CONFORMATION; TETRAHYMENA; THERMODYNAMICS;

TETRAHYMENA;

EID: 0036074219     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838202020216     Document Type: Article

References (45)

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3. Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods
4. Fluorescence-detected stopped flow with a pyrene labeled substrate reveals that guanosine facilitates docking of the 5′ cleavage site into a high free energy binding mode in the Tetrahymena ribozyme
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10. Conformational switches involved in orchestrating the successive steps of group I RNA splicing
11. A preorganized active site in the crystal structure of the Tetrahymena ribozyme
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13. Ribozyme crevices and catalysis
14. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site
15. The importance of being ribose at the cleavage site in the Tetrahymena ribozyme reaction
16. Comparison of pH dependencies of the Tetrahymena ribozyme reactions with RNA 2′-substituted and phosphorothioate substrates reveals a rate-limiting conformational step
17. Binding energy, specificity, and enzymatic catalysis: The circe effect
18. Dissection of the role of the conserved G·U pair in group I RNA self-splicing
19. 2+ and the 2′OH of guanosine on steps required for substrate binding and reactivity with the Tetrahymena ribozyme reveal several local folding transitions
20. A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA
21. A positive entropy change for guanosine binding and for the chemical step in the Tetrahymena ribozyme reaction
22. Guanosine binding to the Tetrahymena ribozyme: Thermodynamic coupling with oligonucleotide binding
23. Isolation of a local tertiary folding transition in the context of a globally folded RNA
24. Mechanistic aspects of enzymatic catalysis: Lessons from comparison of RNA and protein enzymes
25. Quantitating tertiary binding energies of 2′OH groups on the P1 duplex of the Tetrahymena ribozyme: Intrinsic binding energy in an RNA enzyme
26. Structure, recognition and adaptive binding in RNA aptamer complexes
27. Metal ion catalysis in the Tetrahymena ribozyme reaction
28. Ribozyme recognition of RNA by tertiary interactions with specific ribose 2′-OH groups
29. Stereochemical course of catalysis by the Tetrahymena ribozyme
30. Probing the role of metal ions in RNA catalysis: Kinetic and thermodynamic characterization of a metal ion interaction with the 2′-moiety of the guanosine nucleophile in the Tetrahymena ribozyme reaction
31. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction
32. Protonated 2′-aminoguanosine as a probe of the electrostatic environment of the active site of the Tetrahymena group I ribozyme
33. Three distinct metal ions at the active site of the Tetrahymena group I ribozyme
34. Mechanical devices of the spliceosome: Motors, clocks, springs, and things
35. Tertiary interactions with the internal guide sequence mediate docking of the P1 duplex into the catalytic core of the Tetrahymena ribozyme
36. A hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme
37. Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site
38. Guanosine binding required for cyclization of the self-splicing intervening sequence ribonucleic acid from Tetrahymena thermophila
39. Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate
40. A second catalytic metal ion in a group I ribozyme
41. Molecular movement inside the translational engine
42. The role of the cleavage site 2′-OH in the Tetrahymena ribozyme reaction: Evidence for catalysis by hydrogen bond donation to the 3′-leaving group oxygen
43. Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: Enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes