Twister ribozyme
From Wikipedia, the free encyclopedia
| Twister-P5 | |
|---|---|
 Consensus secondary structure and sequence conservation of Type-P5 twister ribozyme | |
| Identifiers | |
| Symbol | Twister-P5 |
| Rfam | RF02684 |
| Other data | |
| RNA type | Gene; Ribozyme |
| GO | GO:0003824 |
| SO | SO:0000374 |
| PDB structures | PDBe |
The twister ribozyme[1] is a catalytic RNA structure capable of self-cleavage. The nucleolytic activity of this ribozyme has been demonstrated both in vivo and in vitro and has one of the fastest catalytic rates of naturally occurring ribozymes with similar function.[2][3] The twister ribozyme is considered to be a member of the small self-cleaving ribozyme family which includes the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), and glmS ribozymes.[3]
In contrast to in vitro selection methods, which have aided in identifying several classes of catalytic RNA motifs, the twister ribozyme was discovered by a bioinformatics approach as a conserved RNA structure of unknown function.[1] The hypothesis that it functions as a self-cleaving ribozyme was suggested by the similarity between genes nearby to twister ribozymes and genes nearby to hammerhead ribozymes,[4] Indeed, the genes located nearby to these two self-cleaving ribozyme classes overlap significantly.[1] Researchers were inspired to name the newly found twister motif due to its resemblance to the Egyptian hieroglyph 'twisted flax'.[1]
Structure
The basic structure of the Oryza sativa twister ribozyme was crystallographically determined at atomic resolution in 2014.[2] The active site of the twister ribozyme is centered in a double-pseudoknot, facilitating a compact fold structure through two long-range tertiary interactions, in partnership with a helical junction.[2] Magnesium is important for secondary structure stabilization of the ribozyme.[3]
Catalytic Mechanism
Similar to other nucleolytic ribozymes, the twister ribozyme selectively cleaves phopshodiester bonds, through an SN2-related mechanism, into a 2',3'-cyclic phosphate and 5' hydroxyl product.[1] Both experimental and modelling evidence have supported a concerted general-acid-base catalysis involving highly conserved adenine (A1) and guanine (G33) bases, where N3 of A1 acts as a proton donor and G33 the general base.[5][6][2] The twister ribozyme generates catalytic activity by specifically orienting the to-be-cleaved P O bond for in-line nucleophilic attack within the active site.[7] Currently, it is known that the rate of reaction of the twister ribozyme is dependent on both pH and temperature.[7][1] Replacements of the pro-S nonbridging oxygen of the scissile phosphate with a thiol group leads to reduced self-cleavage rates, suggesting that the mechanism is not reliant on bound magnesium. Rescue of the thiol-derivative by cadmium cations indicates that divalent metal ions play a role in rate enhancement.[6] A likely mechanism for this is the stabilization of the transition state by reducing electrostatic strain on the substrate strand from the growing negative charge during cleavage.