Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data.

The active centers of the hairpin and VS ribozymes are both generated by the interaction of two internal loops, and both ribozymes use guanine and adenine nucleobases to accelerate cleavage and ligation reactions. The centers are topologically equivalent and the relative positioning of key elements the same. There is good evidence that the cleavage reaction of the VS ribozyme is catalyzed by the guanine (G638) acting as general base and the adenine (A756) as general acid. We now critically evaluate the experimental mechanistic evidence for the hairpin ribozyme. We conclude that all the available data are fully consistent with a major contribution to catalysis by general acid-base catalysis involving the adenine (A38) and guanine (G8). It appears that the two ribozymes are mechanistically equivalent.

[1]  D. Lilley,et al.  The complete VS ribozyme in solution studied by small-angle X-ray scattering. , 2008, Structure.

[2]  A. Ferré-D’Amaré,et al.  Crystal structure of a hairpin ribozyme–inhibitor complex with implications for catalysis , 2001, Nature.

[3]  L. Scott,et al.  Direct Measurement of the Ionization State of an Essential Guanine in the Hairpin Ribozyme , 2009, Nature chemical biology.

[4]  D. Lilley,et al.  Nucleobase participation in ribozyme catalysis. , 2005, Journal of the American Chemical Society.

[5]  A. Ferré-D’Amaré,et al.  Crystal structure of a hepatitis delta virus ribozyme , 1998, Nature.

[6]  W. Scott,et al.  Tertiary Contacts Distant from the Active Site Prime a Ribozyme for Catalysis , 2006, Cell.

[7]  D. Lilley,et al.  The global structure of the VS ribozyme , 2002, The EMBO journal.

[8]  Taekjip Ha,et al.  A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[9]  D. Lilley,et al.  Ribozymes and RNA Catalysis , 2007 .

[10]  D. Lilley,et al.  Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. , 1998, Molecular cell.

[11]  F. Major,et al.  Functional involvement of G8 in the hairpin ribozyme cleavage mechanism , 2001, The EMBO journal.

[12]  D. Lilley,et al.  The A730 loop is an important component of the active site of the VS ribozyme. , 2001, Journal of molecular biology.

[13]  J. Wedekind,et al.  Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation. , 2009, Journal of the American Chemical Society.

[14]  N. Walter,et al.  Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction , 1999, Nature Structural Biology.

[15]  D. Lilley,et al.  Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme. , 2001, Biochemistry.

[16]  D. Lilley,et al.  A guanine nucleobase important for catalysis by the VS ribozyme , 2007, The EMBO journal.

[17]  S. Strobel,et al.  Catalytic importance of a protonated adenosine in the hairpin ribozyme active site. , 2010, Biochemistry.

[18]  M. Fedor,et al.  Rescue of an abasic hairpin ribozyme by cationic nucleobases: evidence for a novel mechanism of RNA catalysis. , 2002, Chemistry & biology.

[19]  R. Collins,et al.  Identification of phosphate groups involved in metal binding and tertiary interactions in the core of the Neurospora VS ribozyme. , 1998, Journal of molecular biology.

[20]  D. Lilley,et al.  Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements. , 2004, RNA.

[21]  M. Fedor,et al.  Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue. , 2004, Journal of molecular biology.

[22]  D. Perrin,et al.  Active site labeling of G8 in the hairpin ribozyme: implications for structure and mechanism. , 2006, Journal of the American Chemical Society.

[23]  A. Ferré-D’Amaré,et al.  Structural Basis of glmS Ribozyme Activation by Glucosamine-6-Phosphate , 2006, Science.

[24]  R. Shippy,et al.  Mutational analysis of loops 1 and 5 of the hairpin ribozyme. , 1998, Biochemistry.

[25]  S. Strobel,et al.  Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping. , 2001, RNA.

[26]  J. Wedekind,et al.  Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme. , 2008, RNA.

[27]  R. Collins,et al.  Evidence for proton transfer in the rate-limiting step of a fast-cleaving Varkud satellite ribozyme , 2007, Proceedings of the National Academy of Sciences.

[28]  Kathryn D. Smith,et al.  Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme. , 2009, Biochemistry.

[29]  J. Grasby,et al.  Purine functional groups in essential residues of the hairpin ribozyme required for catalytic cleavage of RNA. , 1995, Biochemistry.

[30]  D. Lilley,et al.  Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme , 2010, Proceedings of the National Academy of Sciences.

[31]  Jennifer A. Doudna,et al.  A conformational switch controls hepatitis delta virus ribozyme catalysis , 2004, Nature.

[32]  R. Collins,et al.  A secondary-structure model for the self-cleaving region of Neurospora VS RNA. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[33]  S. Strobel,et al.  Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor. , 2007, Chemistry & biology.

[34]  J. Wedekind,et al.  Identification of an imino group indispensable for cleavage by a small ribozyme. , 2009, Journal of the American Chemical Society.

[35]  Structure and activity of the hairpin ribozyme in its natural junction conformation: effect of metal ions. , 1998 .

[36]  D. Lilley,et al.  Nucleobase catalysis in the hairpin ribozyme. , 2006, RNA.

[37]  T L Beattie,et al.  A long‐range pseudoknot is required for activity of the Neurospora VS ribozyme. , 1996, The EMBO journal.

[38]  D. Lilley,et al.  Efficient, pH-dependent RNA ligation by the VS ribozyme in trans. , 2004, Biochemistry.

[39]  B. Golden,et al.  A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage. , 2010, Biochemistry.

[40]  A. Ferré-D’Amaré,et al.  Essential role of an active-site guanine in glmS ribozyme catalysis. , 2007, Journal of the American Chemical Society.

[41]  Emil Alexov,et al.  Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. , 2007, Journal of molecular biology.

[42]  Shawna L. Hiley,et al.  4‐thio‐U cross‐linking identifies the active site of the VS ribozyme , 2002, The EMBO journal.

[43]  A. Ferré-D’Amaré,et al.  Transition State Stabilization by a Catalytic RNA , 2002, Science.

[44]  Harry F. Noller,et al.  A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA , 2008, Nature.

[45]  D. Lilley,et al.  Observation of internal cleavage and ligation reactions of a ribozyme , 2004, Nature Structural &Molecular Biology.

[46]  John M. Burke,et al.  Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site. , 2005, Biochemistry.

[47]  D. Lilley,et al.  Metal ion binding and the folding of the hairpin ribozyme. , 2002, RNA.

[48]  M. Milovanovic,et al.  Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme. , 2003, Acta crystallographica. Section D, Biological crystallography.

[49]  M. Fedor,et al.  Role of an active site adenine in hairpin ribozyme catalysis. , 2005, Journal of molecular biology.

[50]  S. Strobel,et al.  Ionization of a critical adenosine residue in the neurospora Varkud Satellite ribozyme active site. , 2003, Biochemistry.

[51]  Darrin M York,et al.  Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases. , 2008, RNA: A publication of the RNA Society.

[52]  P. Bevilacqua.  Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme. , 2003, Biochemistry.

[53]  R. Tritz,et al.  RNA catalytic properties of the minimum (-)sTRSV sequence. , 1989, Biochemistry.

[54]  J. Piccirilli,et al.  General acid catalysis by the hepatitis delta virus ribozyme , 2005, Nature chemical biology.

[55]  D. Lilley,et al.  Functional group requirements in the probable active site of the VS ribozyme. , 2002, Journal of molecular biology.

[56]  D. Lilley,et al.  Formation of an active site in trans by interaction of two complete Varkud Satellite ribozymes. , 2009, RNA.

[57]  D. Lilley,et al.  Structure, folding and activity of the VS ribozyme: importance of the 2‐3‐6 helical junction , 2001, The EMBO journal.

[58]  W. Scott,et al.  The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. , 1998, Chemistry & biology.

[59]  Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity , 2003, Nature Structural Biology.

[60]  S. Nakano,et al.  General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. , 2000, Science.

[61]  J. Wedekind,et al.  Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer. , 2006, Biochemistry.

[62]  D. Lilley,et al.  Folding of the four-way RNA junction of the hairpin ribozyme. , 1998, Biochemistry.

[63]  S. Strobel,et al.  An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5'- and 3'-termini. , 2001, Nucleic acids research.