Structural insight into the activation of an Arabidopsis organellar C-to-U RNA editing enzyme by active site complementation

RNA-binding pentatricopeptide repeat (PPR) proteins catalyze hundreds of cytidine to uridine RNA editing events in plant organelles; these editing events are essential for proper gene expression. More than half of the PPR-type RNA editing factors, however, lack the DYW cytidine deaminase domain. Genetic analyses have suggested that their cytidine deaminase activity arises by association with a family of DYW1-like proteins that contain an N-terminally truncated DYW domain, but their molecular mechanism has been unclear. Here, we report the crystal structure of the Arabidopsis thaliana DYW1 deaminase domain at 1.8 angstrom resolution. DYW1 has a cytidine deaminase fold lacking the PG box. The internal insertion within the deaminase fold shows an alpha-helical fold instead of the beta-finger reported for the gating domain of the A. thaliana ORGANELLE TRANSCRIPT PROCESSING 86. The substrate-binding pocket is incompletely formed and appears to be complemented in the complex by the E2 domain and the PG box of the interacting PPR protein. In vivo RNA editing assays corroborate the activation model for DYW1 deaminase. Our study demonstrates the common activation mechanism of the DYW1-like proteins by molecular complementation of the DYW domain and reconstitution of the substrate-binding pocket. The crystal structure of DYW1 provides structural insight into the activation mechanism of cytidine deaminase by complementation of the substrate pocket in the DYW domain.

Automated summary

The activation mechanism of DYW1-like proteins is achieved through complementation of the DYW domain and reconstitution of the substrate-binding pocket. This provides structural insight into the activation mechanism of cytidine deaminase.