The structure of the stemloop D subdomain of coxsackievirus B3 cloverleaf RNA and its interaction with the proteinase 3C

Stemloop D (SLID) of the 5' cloverleaf RNA is the cognate ligand of the coxsackievirus B3 (CVB3) 3C proteinase (3C(pro)). Both are indispensable components of the viral replication initiation complex. SLD is a structurally autonomous subunit of the 5' cloverleaf. The SLID structure was solved by NMR spectroscopy to an rms deviation of 0.66 Angstrom (all heavy atoms). SLID contains a novel triple pyrimidine mismatch motif with a central Watson-Crick type C:U pair. SLD is capped by an apical uCACGg tetraloop adopting a structure highly similar to stable cUNCGg tetraloops. Binding of CVB3 3C(pro) induces changes in NMR spectra for nucleotides adjacent to the triple pyrimidine mismatch and of the tetraloop implying them as sites of specific SLD:3C(pro) interaction. The binding of 3C(pro) to SLD requires the integrity of those structural elements, strongly suggesting that 3C(pro) recognizes a structural motif instead of a specific sequence.