Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from?

Abstract

The hammerhead ribozyme was first considered as a metalloenzyme despite persistent inconsistencies between structural and functional data. In the last decade, metal ions were confirmed as catalysts in self-splicing ribozymes but displaced by nucleobases in self-cleaving ribozymes. However, a model of catalysis just relying on nucleobases as catalysts does not fully fit some recent data. Gathering and comparing data on metal ions in self-cleaving and self-splicing ribozymes, the roles of divalent metal ions and nucleobases are revisited. Hypothetical models based on cooperation between metal ions and nucleobases are proposed for the catalysis and evolution of this prototype in RNA catalysis.

Figure 1

HHRz motifs and variants. (A) HH-1 motif (Rfam ID: RF00163). (B) HH-3 motif (Rfam ID: RF00008). (C) HH-1 extended motif from Schistosoma mansoni [42]. (D) HH-1 minimal motif truncated from the lucerne transient streak virus (PDB ID: 301D [23]).

Figure 2

Stereo views of metal binding sites in the X-ray structures of self-cleaving and self-splicing ribozymes.

Figure 3

Catalytic Strategies in the Transphosphoryl Reaction of RNase A and Self-Cleaving Ribozymes.

Figure 4

Hypothetical Models for the Nucleobase-Metal Catalysis in the Hammerhead Ribozyme.

Figure 5

Schematic reaction coordinate indicating the possible roles of Mg²⁺ and nucleobases as catalysts in ‘minimal’ and ‘extended’ ancestor variants of the HHRz.