The bipartite architecture of the sRNA in an archaeal box C/D complex is a primary determinant of specificity

The archaeal box C/D sRNP, the enzyme responsible for 2′-O-methylation of rRNA and tRNA, possesses a nearly perfect axis of symmetry and bipartite structure. This RNP contains two platforms for the assembly of protein factors, the C/D and C′/D′ motifs, acting in conjunction with two guide sequences to direct methylation of a specific 2′-hydroxyl group in a target RNA. While this suggests that a functional asymmetric single-site complex complete with guide sequence and a single box C/D motif should be possible, previous work has demonstrated such constructs are not viable. To understand the basis for a bipartite RNP, we have designed and assayed the activity and specificity of a series of synthetic RNPs that represent a systematic reduction of the wild-type RNP to a fully single-site enzyme. This reduced RNP is active and exhibits all of the characteristics of wild-type box C/D RNPs except it is nonspecific with respect to the site of 2′-O-methylation. Our results demonstrate that protein–protein crosstalk through Nop5p dimerization is not required, but that architecture plays a crucial role in directing methylation activity with both C/D and C′/D′ motifs being required for specificity.