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.
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.
Folding of the HDV antigenomic ribozyme pseudoknot structure deduced from long-range photocrosslinks.
A trans-acting system designed in order to explore the three-dimensional structure of the anti-genomic HDV ribozyme, it is demonstrated that RzANT is able to cleave specifically the RNA substrate as well as a deoxysubstrate analogue containing a single ribocytidine at the cleavage site (position -1).
Modeling active RNA structures using the intersection of conformational space: application to the lead-activated ribozyme.
A three-dimensional modeling protocol was used to propose a structure for this ribozyme that suggests an in-line SN2 attack mechanism and predicts two Pb2+ binding sites, and is generally applicable in modeling RNAs whenever the catalytic or binding activity of structural analogues is known.
Construction of hairpin ribozymes with a three-way junction.


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.
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.
Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA.
X-ray diffraction data from monoclinic crystals of yeast tRNAPhe soaked in dilute lead(II) acetate solutions suggests that the cleavage involves removal of the proton from the 2'-OH of ribose-17 by a Pb(II)-bound hydroxyl group.
Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes.
This finding gives further evidence for the hypothesis that the magnesium ion is bound to the pro-R oxygen in the transition state of the hammerhead cleavage reaction.
Life Before DNA. (Book Reviews: The RNA World. The Nature of Modern RNA Suggests a Prebiotic RNA World.)
This book discusses RNA Folding, Unfolding, and Dynamics, One Molecule at a Time, and a Modular and Hierarchical approach for All-Atom RNA Modeling.
Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees
The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 90 degrees. This
Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration.
The results are consistent with transesterification occurring by an inline SN2(P) attack of the 2'-hydroxyl group in the autolytic processing reactions of both polarities of the satellite RNA.