Naturally existing small catalytic RNAs include hammerhead, hairpin, hepatitis delta virus (HDV) and Varkud satellite (VS) ribozymes. The structures of small ribozymes are simple but diversified. Hammerhead ribozyme consists of 3 short helices and a conserved joint chain. Hairpin ribozyme's deeply buried active region is made up of two side-by-side helices. HDV ribozyme folds to a double-knot structure which contains 5 helix arms. VS ribozyme is made up of 5 helix regions and two joint regions. These ribozymes appear to exploit different cleavage mechanisms which depend upon their individual architectures. Metal ions and nucleobases might be candidates for participants in acid/base catalysis. Hammerhead ribozyme has a basic requirement for divalent metal ions, such as Mg2+ ions, to complete it's function. However, hairpin ribozyme can be considered as a distinct one that does not require metal ions as cofactors. In the genomic HDV ribozyme, a metal ion functions as a general base and a cytosine residue functions as a general acid.
WANG Jun-Feng, LIAO Xiang-Ru, FU Wei. Structures and Catalytic Mechanisms of Small Ribozymes[J]. Progress in Biochemistry and Biophysics,2002,29(5):674-677
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