9KFY

Crystal structure of synthetic PPR-DYW in its RNA-free state

Summary for 9KFY

• Entry DOI: 10.2210/pdb9kfy/pdb
• Descriptor: Synthetic PPR-DYW protein, GLYCEROL, ZINC ION, ... (4 entities in total)
• Functional Keywords: rna binding protein, pentatricopeptide repeat deaminase, plant rna editing, hydrolase
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 68637.57

Authors

Aoyama, R.,Gutmann, B.,Ichinose, M.,Yagi, Y.,Nakamura, T.,Kakuta, Y.,Teramoto, T. (deposition date: 2024-11-07, release date: 2025-11-12, Last modification date: 2026-07-15)

Primary citation

Teramoto, T.,Urushihara, R.,Aoyama, R.,Okada, A.,Ichinose, M.,Yagi, Y.,Nakamura, T.,Gutmann, B.,Kakuta, Y.
Structural basis of plant organelle C-to-U RNA editing by PPR-DYW proteins.
Nat Commun, 17:-, 2026

PubMed Abstract: Plants possess a unique C-to-U RNA editing mechanism mediated by PPR-DYW proteins, wherein the PPR domain recognizes specific RNA sequences while the DYW deaminase domain precisely edits the target C base-a process essential for functional protein expression in plant chloroplasts and mitochondria. The coordination of these two domains is considered crucial for precise RNA editing. In nature, this site-specific and precise base editing by PPR-DYW proteins distinguishes them from other base-editing deaminases. However, the absence of structures containing both PPR and DYW domains has limited our understanding of the precise RNA-editing mechanism of PPR-DYW proteins. Here, we present crystal structures of the consensus PPR-DYW (consPPR-DYW) protein, a representative of the PPR-DYW proteins, in both RNA-free and target RNA-bound states. Comparison between these states demonstrates domain movements upon target RNA binding, whereby the PPR domain accommodates the upstream sequence of the target C base in the proper conformation for editing while the DYW domain is optimally positioned for precise C-to-U conversion. These results, combined with comprehensive biochemical analyses, provide the foundation for a mechanistic model that explains the coordinated action of the PPR and DYW domains in achieving precise C-to-U editing.

PubMed: 42045200
DOI: 10.1038/s41467-026-72391-y

Experimental method

X-RAY DIFFRACTION (2.26 Å)