Hairpin Ribozyme

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Contents 1 Hairpin Ribozyme Overview 2 Structure 3 Kinetics 4 References

Hairpin Ribozyme Overview

spinqualitylabelsall models Crystal Structure of the Hairpin Ribozyme in the catalytically-active conformation (PDB entry 1m5k) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Anything in this section will appear adjacent to the 3D structure and will be scrollable. The hairpin ribozyme is a member of a small family of RNA endonucleases that includes hammerhead, hepatitis delta, and Neurospora VS. Endonucleases are enzymes that cleave phosphodiester bonds within polynucleotide chains. This group of endonucleases cleave RNA substrates in a reversible reaction that generates a 2', 3'-cyclic phosphate and a 5'-hydroxyl termini.[1] The hairpin ribozyme was discovered in the negative strand of the tobacco ringspot virus (TRSV) satellite RNA. Study of hairpin ribozyme reaction mechanisms provided early evidence that ribozymes are able to exploit a variety of strategies, just like protein enzymes. But, the hairpin ribozyme has a unique characteristic. Unlike other ribozymes, the hairpin ribozyme does not require metal ions for cleavage or ligation of substrate RNA.

Structure

In the transition state, the

The secondary structure of the hairpin ribozyme contains two independently folding domains, called A and B. In each domain there is an internal loop flanked by two helices(H1 and H2 in domain A and H3 and H4 in domain B). The RNA substrate is bound in domain A through Watson-Crick base pairs in H1 and H2. Once bound to domain A, the substrate is reversibly cleaved. Linkers of varying lengths were inserted between the 5' end of the substrate and the 3' end of the ribozyme in order to test what proximity is preferred by the two domains. The results of the test showed that the two domains prefer to be relatively close to one another and use H2 and H3 as a sort of hinge. In the naturally occurring hairpin ribozyme, this hinge is occupied by a four-way junction, which is believed to regulate inter-domain interactions by alternative stacking of helices.^[2]

Kinetics

There are at least four steps in the reaction pathway of the hairpin ribozyme. They are: (1) substrate binding to ribozyme, (2) cleavage in the ribozyme-substrate complex, (3) release of 5' products, and (4) release of 3' products. The rates and equilibrium constants for individual steps have been studied. Substrate binding can reach a minimum of <math>6*10^6 M^-1 min^-1</math>

References

1. ↑ Fedor MJ. Structure and function of the hairpin ribozyme. J Mol Biol. 2000 Mar 24;297(2):269-91. PMID:10715200 doi:http://dx.doi.org/10.1006/jmbi.2000.3560
2. ↑ Walter NG, Burke JM. The hairpin ribozyme: structure, assembly and catalysis. Curr Opin Chem Biol. 1998 Feb;2(1):24-30. PMID:9667918