7w86 | pdb_00007w86

Crystal structure of the DYW domain of DYW1

spinqualitylabelsall models 7w86, resolution 1.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7w86 is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.8Å Ligands: ACT, EDO, GOL, SO4, ZN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function PPR74_ARATH Plays a major role in single RNA editing events in chloroplasts. Acts as a site-recognition transacting factor involved in the edition of the site 1 of ndhD (ndhD-1 site corresponding to cytidine-2), which is a plastid-encoded subunit of the NADH-plastoquinone oxidoreductase. The interaction with CRR4 is required for its function in editing the ndhD-1 site. Publication Abstract from PubMed 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 A 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. Structural insight into the activation of an Arabidopsis organellar C-to-U RNA editing enzyme by active site complementation.,Toma-Fukai S, Sawada Y, Maeda A, Shimizu H, Shikanai T, Takenaka M, Shimizu T Plant Cell. 2023 May 29;35(6):1888-1900. doi: 10.1093/plcell/koac318. PMID:36342219 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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