Anticodon-like loop-mediated dimerization in the crystal structures of HdV-like CPEB3 ribozymes

Abstract

ABSTRACTCytoplasmic polyadenylation element-binding (CPEB) proteins are involved in many different cellular processes including cell division, synaptic plasticity, learning, and memory. A highly conserved, short mammalian ribozyme has been found within the second intron of the CPEB3 gene. Based on its cleavage mechanism and structural features, this ribozyme belongs to the hepatitis delta virus (HDV)-like ribozyme family. Here, we present the first crystallographic structures of human and chimpanzee CPEB3 ribozymes both confirming the general topology of the HDV ribozyme with two parallel co-axial helical stacks. However, the residues involved in the formation of the characteristic double-nested pseudoknot P1.1 instead participate in a seven nucleotides loop with a conformation identical to the one found in the anticodon (AC) loop of tRNAs. The conformation of the loop supports the formation of a 4 base pair helix by interacting with an AC-like loop from a symmetry-related ribozyme leading to ribozyme dimer formation. Comparing the present crystal structures to the one from the genomic HDV ribozyme shows how nucleotides with different identities adopt distinct behaviours. These new snapshots suggest unforeseen relationships between the genomic, the antigenomic versions of the HDV ribozyme and the CPEB3 ribozyme.