Three-dimensional structure of a hammerhead ribozyme

The hammerhead ribozyme is a small catalytic RNA motif made up of three base-paired stems and a core of highly conserved, non-complementary nucleotides essential for catalysis. 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 that the core has two structural domains. The first domain is formed by the sequence 5′-CUGA following stem I and is a sharp turn identical to the uridine turn of transfer RNA, whereas the second is a non-Watson–Crick three-base-pair duplex with a divalent-ion binding site. The phosphodiester back-bone of the DNA inhibitor strand is splayed out at the phosphate 5′ to the cleavage site. The structure indicates that the ribozyme may destabilize a substrate strand in order to facilitate twisting of the substrate to allow cleavage of the scissile bond.

[1]  A. Rich,et al.  Structural domains of transfer RNA molecules. , 1976, Science.

[2]  R Cedergren,et al.  Numbering system for the hammerhead. , 1992, Nucleic acids research.

[3]  O. Uhlenbeck,et al.  Thiophosphate interference experiments locate phosphates important for the hammerhead RNA self-cleavage reaction. , 1990, Nucleic acids research.

[4]  J. M. Buzayan,et al.  Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA , 1986, Nature.

[5]  R. Cedergren,et al.  Mixed deoxyribo- and ribo-oligonucleotides with catalytic activity , 1990, Nature.

[6]  O. Uhlenbeck,et al.  Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism. , 1993, Biochemistry.

[7]  E. Ohtsuka,et al.  Effects of phosphorothioate and 2-amino groups in hammerhead ribozymes on cleavage rates and Mg2+ binding. , 1991, Biochemistry.

[8]  J. M. Buzayan,et al.  Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration. , 1990, Nucleic acids research.

[9]  Wolfgang Kabsch,et al.  Evaluation of Single-Crystal X-ray Diffraction Data from a Position-Sensitive Detector , 1988 .

[10]  T. Tuschl,et al.  Importance of exocyclic base functional groups of central core guanosines for hammerhead ribozyme activity. , 1993, Biochemistry.

[11]  G D Stormo,et al.  Sequence requirements of the hammerhead RNA self-cleavage reaction. , 1990, Biochemistry.

[12]  M. Gait,et al.  Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes. , 1991, Nucleic acids research.

[13]  R. Symons,et al.  Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites , 1987, Cell.

[14]  C. Deluca-Flaherty,et al.  Crystals of a hammerhead ribozyme. , 1993, The Journal of biological chemistry.

[15]  O. Uhlenbeck,et al.  Characterization of deoxy- and ribo-containing oligonucleotide substrates in the hammerhead self-cleavage reaction. , 1990, Biochimie.

[16]  L. McLaughlin,et al.  Importance of specific purine amino and hydroxyl groups for efficient cleavage by a hammerhead ribozyme. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[17]  R. Cedergren,et al.  The hammerhead RNA domain, a model ribozyme. , 1993, Biochimica et biophysica acta.

[18]  M. Gait,et al.  The role of the exocyclic amino groups of conserved purines in hammerhead ribozyme cleavage. , 1992, Biochemical and biophysical research communications.

[19]  O. Uhlenbeck,et al.  Role of divalent metal ions in the hammerhead RNA cleavage reaction. , 1991, Biochemistry.

[20]  R. Symons,et al.  Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. , 1986, Nucleic acids research.

[21]  W. Gerlach,et al.  Simple RNA enzymes with new and highly specific endoribonuclease activities , 1988, Nature.

[22]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[23]  D. Turner,et al.  Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics. , 1993, Biochemistry.

[24]  D. Williams,et al.  Function of specific 2'-hydroxyl groups of guanosines in a hammerhead ribozyme probed by 2' modifications. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[25]  O. Uhlenbeck,et al.  A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. , 1994, Biochemistry.

[26]  J. M. Buzayan,et al.  Nucleic Acids Research Nucleotide sequence and newly formed phosphodJester bond of spontaneously Ugated satellite tobacco ringspot virus RNA , 2005 .

[27]  J. M. Buzayan,et al.  Autolytic Processing of Dimeric Plant Virus Satellite RNA , 1986, Science.

[28]  O. Uhlenbeck.  A small catalytic oligoribonucleotide , 1987, Nature.

[29]  L. McLaughlin,et al.  Importance of specific guanosine N7-nitrogens and purine amino groups for efficient cleavage by a hammerhead ribozyme. , 1993, Biochemistry.

[30]  J. Grasby,et al.  The synthesis of oligoribonucleotides containing O6-methylguanosine: the role of conserved guanosine residues in hammerhead ribozyme cleavage. , 1993, Nucleic acids research.

[31]  The refinement of the heavy-atom parameters in the presence of non-crystallographic symmetry , 1976 .

[32]  D. Mckay,et al.  Crystals and a low resolution structure of interleukin-2. , 1987, The Journal of biological chemistry.

[33]  G. Sheldrick.  Phase annealing in SHELX-90: direct methods for larger structures , 1990 .

[34]  R. Symons,et al.  Mutagenesis analysis of a self-cleaving RNA. , 1989, Nucleic acids research.

[35]  T. Tuschl,et al.  Hammerhead ribozymes: importance of stem-loop II for activity. , 1993, Proceedings of the National Academy of Sciences of the United States of America.