Hairpin ribozyme structure

BANERJEE ETAL. Hairpin Ribozyme Structure and Dynamics... 

The ribozymes were widely modified and can be further subdivided according to their structural features in group I ribozymes, hammerhaed ribozymes, hairpin ribozymes, ribonucelase P (RNase P), and hepatitis delta virus ribozymes. 

Figure 14-7. Snapshots of the active site structures near the transition state of (top) the nucleophilic attack and (bottom) the exocyclic cleavage for the in-line monoanionic O2p mechanism of cleavage transesterification in the hairpin ribozyme. The yellow and red colored cartoon is for the substrate and ribozyme strands, respectively, and water molecules interacting with non-bridging oxygens and O5/ are shown...

However, there are a number of other miscellaneous biological roles played by this complex. The [Co(NH3)6]3+ ion has been shown to inhibit the hammerhead ribozyme by displacing a Mn2+ ion from the active site.576 However, [Co(NH3)6]3+ does not inhibit ribonuclease H (RNase),577 topoisomerase I,578 or hairpin ribozyme,579 which require activation by Mg2+ ions. The conclusions from these studies were that an outer sphere complex formation between the enzyme and Mgaq2+ is occuring rather than specific coordination of the divalent ion to the protein. These results are in contrast to DNase I inhibition by the same hexaammine complex. Inhibition of glucose-induced insulin secretion from pancreatic cells by [Co(NH3)6]3+ has been found.580 Intracellular injection of [Co(NH3)6]3+ into a neurone has been found to cause characteristic changes to the structure of its mitochondria, and this offers a simple technique to label neuronal profiles for examination of their ultrastructures.581... 

Burke JM, Butcher SE, SargueU B (1996). Structural analysis and modifications of the hairpin ribozyme, p 129-144. In Eckstein F, Lilley DMJ (ed) Catalytic RNA, vol. 10. Springer, Berlin Heidelberg New York... 

Fig. 1A-F The two-dimensional structures of various ribozymes. The ribozyme or intron portion is printed in black. The substrate or exon portion is printed in gray. Arrows indicate sites of cleavage by ribozymes A (left) the two-dimensional structure of a hammerhead ribozyme and its substrate. Outlined letters are conserved bases that are involved in catalysis right) The y-shaped structure of the hammerhead ribozyme-sub-strate complex B-F the two-dimensional structures of a hairpin ribozyme, the genomic HDV ribozyme, a group I ribozyme from Tetrahymena, a group II ribozyme from S. cer-evisiae (aiy5), and the ribozyme of RNase P from E. coli...

Smaller self-cleaving RNAs have been found among plant viruses and viroids. Many of them have a common catalytic core which can be converted into 30- to 40-nucleotide ribozymes. Only 17 nucleotides and three hydrogen-bonded helical stems are required to form the self-cleaving "hammerhead" domain, which has a structural similarity to the catalytic core of the Tetrahymena ribozyme. The hammerhead ribozymes (Fig. 12-27) represent one form of small ribozyme.793-797 Another is the hairpin ribozyme shown in Fig. 

Figure 4.2 The hammerhead and hairpin ribozymes. Secondary structures for both the hammerhead and hairpin ribozymes are depicted. N=any nucleotide, R=Purine and Y=Pyrimidine. A diagram of the tertiary structure of the hammerhead ribozyme is depicted above the secondary structure model. The corresponding stems I, II and III in both structures are shown. In the hammerhead ribozyme H=A, C or U at the cleavage site. In the hairpin ribozymes HI, H2, etc. refer to the helical regions of the RNA structure.

Comparative gel electrophoresis analysis of the 4H junction of U1 snRNA showed the junction adopted a coaxially stacked structure with almost perpendicular axes (Fig. 7.3). This result was very recently confirmed crystallographically (Pomeranz-Krummel et al., 2009). Perhaps the most extensively studied 4H junction in RNA is that of the hairpin ribozyme,... 

Rupert, P. B., and Ferre-D Amare, A. R. (2001). Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410, 780-786. 

Walter, F., Murchie, A. I. H., Thomson, J. B., and Lilley, D. M. J. (1998c). Structure and activity of the hairpin ribozyme in its natural junction conformation effect of metal ions. Biochemistry 37(40), 14195—14203. 

Klostermeier, D., and Millar, D. P. (2001). Tertiary structure stability of the hairpin ribozyme in its natural and minimal forms Different energetic contributions from a ribose zipper motif. Biochemistry 40, 11211—11218. 

Pljevaljcic, G., Millar, D. P., and Deniz, A. A. (2004). Freely diffusing single hairpin ribozymes provide insights into the role of secondary structure and partially folded states in RNA folding. Biophys. J. 87, 457—467. 

Walter, N. G., Hampel, K. J., Brown, K. M., and Burke, J. M. (1998c). Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer. EMBOJ. 17, 2378-2391. 

Walter, N. G., Burke, J. M., and Millar, D. P. (1999). Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction. Nat. Struct. Biol. 6, 544—549. 

Pljevaljcic, G., Klostermeier, D., et al. (2005). The tertiary structure of the hairpin ribozyme is formed through a slow conformational search. Biochemistry 44(12), 4870-4876. 

Construction of a hairpin ribozyme targeting more than one site within the substrate RNA also yields further insight into the structural limits of hairpin ribozyme-catalyzed RNA processing and can provide information on the structural and mechanistic requirements of catalysis. 

Fig. 5.2.5. Secondary structure of the conventional hairpin ribozyme HP-WT. The arrow denotes the cleavage site. The four helices (H-1 through H-4) are marked by bars.

Conventional and reverse-joined hairpin ribozymes as described above can be combined in one molecule to create a twin ribozyme. Their use is, however, limited by the specific structure. Because folding into the active conformation requires a bend between helix 2 and helix 3 in the conventional hairpin ribozyme, and between helix 1 and helix 4 in the reverse-joined hairpin ribozyme, these helices form a sort of hinge and are, therefore, not susceptible to arbitrary changes. Whereas helix 1 in HP-WT can be extended without distortion of tertiary folding, the situation in the reverse-joined hairpin ribozyme is the opposite, helix 2 can be extended,... 

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