Hairpin ribozyme , catalysis

Case Study Chemical Steps of Catalysis in Hairpin Ribozyme... 

In contrast, the hairpin ribozyme (HPR) [107, 108], which catalyzes the reversible, site-specific phosphodiester bond cleavage of an RNA substrate, is unique in that the chemical steps of the reaction do not require involvement of a divalent metal ion [107-111]. This lack of an explicit metal ion requirement [112] makes the hairpin ribozyme an ideal target for theoretical studies aimed to characterize the contribution of generalized solvation provided by the solvated ribozyme on catalysis. 

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...

Chowrira, B. M., A. Berzal-Herranz, and J. M. Burke, Novel guanosine requirement for catalysis by the hairpin ribozyme. Nature 354 320-323, 1991. In some cases the guanine amino group serves a catalytic role in selfsplicing. 

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. 

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. 

Interestingly, specific M +-nucleic acid interactions determined in solution for the hairpin ribozyme by spectroscopic and chemical interference methods were not later found in their X-ray crystal stmctures. Even more confusing were results of X-ray crystallography " and initial solution experiments, which both determined up to two, presumably functionally important Mg + ions in the catalytic center of the hammerhead ribozyme. However, as demonstrated recently in biochemical experiments in solution, neither of these ribozymes require either inner- or outer-sphere interactions with particular metal ions for catalysis. ... 

B.M. Chowrira, A. Berzalherranz, J.M. Burke, Novel Guanosine Requirement for Catalysis by the Hairpin Ribozyme , Nature, 354, 320 (1991)... 

Wilson TJ, Nahas M, Ha T, Lilley DM. Folding and catalysis of the hairpin ribozyme. Biochem. Soc. Trans. 2005 33 461-465. 

Bevilacqua PC. Mechanistic considerations for general acid-base catalysis by RNA revisiting the mechanism of the hairpin ribozyme. Biochemistry 2003 42 2259-2265. 

In hairpin ribozyme, the nucleobase of G8 is immediately adjacent to the attacking 2 -OH of Al and could play a direct role in catalysis. The HDV ribozyme provides a well-characterized example of nucleobase catalysis. The structure of the ribozyme-product complex has been solved by crystallography (Ferre-d Amare et al., 1998), revealing a deep cleft containing the site of cleavage. It also contains an essential cytosine base (C75 in the... 

Lilley DM (2008) Ribozymes and RNA Catalysis, chap. The Hairpin and Varkud Satellite Ribozymes, 66-91, RSC Biomolecular Series, RSC Publishing, Cambridge. 

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