Structure of the eukaryotic atypical RIO kinases reveals ATPase‐dependent mechanism in ribosome biogenesis

Abstract

RIO kinases are ancient atypical protein kinases essential for the final maturation step of the small subunit of the ribosome. The crystal structures of two eukaryotic RIO kinases, Rio2 from Chaetomium thermophilum and human RioK1, in the presence of ATP, were determined to 2.5 and 2.8 Å respectively. Unexpectedly, a novel phosphoaspartate intermediate was observed in both structures. Acyl‐phosphate intermediates, observed in P‐type ATPases, are unusual for serine protein kinases. Prompted by this new information, we show that RIO kinases have significant ATPase activity. Additionally, docking of the eukaryotic Rio2 kinase into a reported cryo‐electron microscopy map of the pre‐40S particles and yeast genetic studies show that although catalytic activity is required for function, the active site is inaccessible when the RIO domain is bound to the pre‐ribosome. A new model for the functional mechanism of the RIO kinases is therefore suggested that includes a role for a transient intermediate and ATPase activity in pre‐40S maturation. We propose that RIO kinases function not as protein kinases, but as ATPases that sense pre‐40S conformational change and drive particles to maturation. These data collectively provide surprising new insight into the role of RIO kinases in ribosome biogenesis.