The crystal structure of an AII-RNAhammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage

  title={The crystal structure of an AII-RNAhammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage},
  author={William G. Scott and John T. Finch and Aaron Klug},
NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis.
A model for metal-binding in the leadzyme is proposed in which a lead ion binds to a bulged guanine base that is critical for leadzyme function.
Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site.
The dynamic properties of the internal loop and details of the high-resolution structure support the view that the hairpin structure represents a ground state, which has to undergo a conformational change prior to cleavage.
The hammerhead ribozyme: structure, catalysis, and gene regulation.
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
The Hammerhead Ribozyme Structure Brought in Line
A novel crystal structure of the hammerhead ribozyme has just been reported, and this should help to clarify a long-standing debate on the mechanism of catalysis, which gave rise to presumably the longest- Standing debate in the ribo enzyme field.
Probing the Cleavage Activity of the Hammerhead Ribozyme Using Analog Complexes
The hammerhead ribozyme is a relatively small RNA catalyst that is derived from a structural motif present in the RNA genomes of several plant pathogens, where it is believed that RNA-mediated cleavage events are an essential step in the viroid’s replication pathway.
Crystallographic analysis of a hammerhead ribozyme variant and its impact on catalytic activity
It is suggested that hammerhead ribozyme substituted with adenine for the general base may compete between two conformational states: an active state in which A12 is situated for deprotonation of the 2'H of C17; and an inactive state inWhich A12 makes a non-canonical base pair A9, causing a perturbation in the active site, disrupting metal ion binding.
Structure-function relationships in RNA and RNP enzymes: recent advances.
The structural biology of ribozymes and ribonucleoprotein (RNP) enzymes is now sufficiently advanced that a true dialogue between structural and functional studies is possible. In this review, we
An ultraviolet crosslink in the hammerhead ribozyme dependent on 2-thiocytidine or 4-thiouridine substitution.
It is demonstrated that a unique crosslink can be induced in the hammerhead with 2-thiocytidine or 4-thiouridine substitution at different locations within the conserved core, suggesting that the structure trapped by the crosslink may be relevant to the catalytically active solution structure of the hammer head ribozyme.
The Varkud satellite ribozyme.
The VS ribozyme is the largest nucleolytic ribo enzyme, for which there is no crystal structure to date, and A756, a particularly critical nucleotide, is a strong candidate for nucleobase participation in the catalytic chemistry.


Three-dimensional structure of a hammerhead ribozyme
The X-ray crystallographic structure of a hammerhead RNA–DNA ribozyme-inhibitor complex at 2.6 Å resolution reveals that the base-paired stems are A-form helices and the core has two structural domains.
Sequence requirements of the hammerhead RNA self-cleavage reaction.
The refined consensus hammerhead resulting from this work was used to identify potential hammerheads present in a variety of Escherichia coli gene sequences, suggesting that the hammerhead contains few, if any, replaceable tertiary interactions as are found in tRNA.
The roles of the conserved pyrimidine bases in hammerhead ribozyme catalysis: evidence for a magnesium ion-binding site.
The kinetic properties of the variants described here are consistent with several key interactions seen in the crystals, in particular they provide experimental support for the assignment of the proposed catalytically active magnesium ion-binding site.
Energetics of RNA cleavage: implications for the mechanism of action of ribozymes.
A new class of ribozymes produce 2',3'-cyclic phosphate upon self-catalyzed cleavage of RNA molecules, similar to those observed during enzymatic (RNase-catalyzed) as well as non-enzymatic hydrolyses
Effects of phosphorothioate and 2-amino groups in hammerhead ribozymes on cleavage rates and Mg2+ binding.
The reaction pathway and a model for Mg2+ binding to the hammerhead ribozyme are presented and it is shown that 1 mol of Mg 2+ binds to the pro-R oxygen of phosphate.
A crystallographic study of metal-binding to yeast phenylalanine transfer RNA.
Three-Dimensional Tertiary Structure of Yeast Phenylalanine Transfer RNA
The 3-angstrom electron density map of crystalline yeast phenylalanine transfer RNA has provided us with a complete three-dimensional model which defines the positions of all of the nucleotide residues in the moleclule, which explains, in a simple and direct fashion, chemical modification studies of transfer RNA.
Pb(II)-catalysed cleavage of the sugar–phosphate backbone of yeast tRNAPhe—implications for lead toxicity and self-splicing RNA
A possible mechanism for the cleavage reaction of Pb(II)–tRNAPhe derivative is formulated and some general ideas on the action of metal ions on nucleic acids are presented.
Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA.
Consideration of several possible mechanisms for the reaction, taking into account the biochemical and crystallographic facts presented above, suggests that the cleavage involves removal of the proton from the 2'-OH of ribose-17 by a Pb(II)-bound hydroxyl group.