Capturing the Structure of a Catalytic RNA Intermediate: The Hammerhead Ribozyme

The crystal structure of an unmodified hammerhead RNA in the absence of divalent metal ions has been solved, and it was shown that this ribozyme can cleave itself in the crystal when divalent metal ions are added. This biologically active RNA fold is the same as that found previously for two modifie...

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Bibliographic Details
Published in:Science (American Association for the Advancement of Science) 1996-12, Vol.274 (5295), p.2065-2069
Main Authors: Scott, William G., Murray, James B., John R. P. Arnold, Stoddard, Barry L., Klug, Aaron
Format: Article
Language:English
Subjects:
Analytical, structural and metabolic biochemistry
Base Sequence
Biological and medical sciences
Catalytic RNA
Chemical bases
Crystal structure
Crystallization
Crystallography, X-Ray
Crystals
Data Collection
Enzymes
Freezing
Fundamental and applied biological sciences. Psychology
Hydrogen bonds
Hydrogen-Ion Concentration
Ions
Literary Devices
Magnesium - metabolism
Manganese - metabolism
Metal ions
Models, Molecular
Nucleic Acid Conformation
Nucleic acids
Oxygen
Phosphates
Physiological aspects
Ribonucleic acid
RNA
RNA, Catalytic - chemistry
RNA, Catalytic - metabolism
Rna, ribonucleoproteins
Scientific Concepts
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Summary:The crystal structure of an unmodified hammerhead RNA in the absence of divalent metal ions has been solved, and it was shown that this ribozyme can cleave itself in the crystal when divalent metal ions are added. This biologically active RNA fold is the same as that found previously for two modified hammerhead ribozymes. Addition of divalent cations at low pH makes it possible to capture the uncleaved RNA in metal-bound form. A conformational intermediate, having an additional Mg(II) bound to the cleavage-site phosphate, was captured by freeze-trapping the RNA at an active pH prior to cleavage. The most significant conformational changes were limited to the active site of the ribozyme, and the changed conformation requires only small additional movements to reach a proposed transition-state.
ISSN:0036-8075
1095-9203
DOI:10.1126/science.274.5295.2065