Leadzyme

Leadzyme is a small ribozyme (catalytic RNA), which catalyzes the cleavage of a specific phosphodiester bond. It was discovered using an in-vitro evolution study where the researchers were selecting for RNAs that specifically cleaved themselves in the presence of lead. However, since then, it has been discovered in several natural systems. Leadzyme was found to be efficient and dynamic in the presence of micromolar concentrations of lead ions. Unlike in other small self-cleaving ribozymes, other divalent metal ions cannot replace Pb²⁺ in the leadzyme. Due to obligatory requirement for a lead, the ribozyme is called a metalloribozyme.

Leadzyme has been subjected to extensive biochemical and structural characterization. The minimal secondary structure of leadzyme is surprisingly very simple . It comprises an asymmetric internal loop composed of six nucleotides and a helical region on each side of the internal loop. The cleavage site of leadzyme is located within a four-nucleotide long asymmetric internal loop that also consists of RNA helices on its both sides. This is shown in top figure on right, which is the secondary structure of leadzyme generated using mfold. The structures of leadzyme have also been solved using X-ray crystallography and NMR. The crystal structures of the two conformations of leadzyme are shown in the lower figure on right.

Leadzyme is thought to perform catalysis using a two-step mechanism. In the first step of the reaction, the phosphodiester bond is cleaved into two products: 5’ product terminating in 2’3’ cyclic phosphate and the 3’ product in 5’ hydroxyl. This step is similar to other small self-cleaving ribozymes such as the Hammerhead ribozyme and HDV ribozyme. Both of those ribozymes generate a product, which contain a 2’, 3’ -cyclic phosphate. However, in leadzyme this product is just an intermediate. In the second step of this reaction pathway, the 2’ 3’ -cyclic phosphate undergoes hydrolysis to form 3’ monophosphate. This mode of catalysis is similar to how ribonucleases (proteins) function rather than any known small self-cleaving ribozyme.

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