7O4F

The DYW domain of A. thaliana OTP86 in its active state

Summary for 7O4F

• Entry DOI: 10.2210/pdb7o4f/pdb
• Related: 7O4E
• Descriptor: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic, ZINC ION (3 entities in total)
• Functional Keywords: cytidine deaminase, hydrolase
• Biological source: Arabidopsis thaliana (Mouse-ear cress)
• Total number of polymer chains: 4
• Total formula weight: 64589.23

Authors

Weber, G.,Palm, G.J.,Takenaka, M.,Barthel, T.,Feiler, C.,Weiss, M.S. (deposition date: 2021-04-06, release date: 2021-06-30, Last modification date: 2024-05-01)

Primary citation

Takenaka, M.,Takenaka, S.,Barthel, T.,Frink, B.,Haag, S.,Verbitskiy, D.,Oldenkott, B.,Schallenberg-Rudinger, M.,Feiler, C.G.,Weiss, M.S.,Palm, G.J.,Weber, G.
DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis.
Nat Catal, 4:510-522, 2021

PubMed Abstract: RNA editosomes selectively deaminate cytidines to uridines in plant organellar transcripts-mostly to restore protein functionality and consequently facilitate mitochondrial and chloroplast function. The RNA editosomal pentatricopeptide repeat proteins serve target RNA recognition, whereas the intensively studied DYW domain elicits catalysis. Here we present structures and functional data of a DYW domain in an inactive ground state and activated. DYW domains harbour a cytidine deaminase fold and a C-terminal DYW motif, with catalytic and structural zinc atoms, respectively. A conserved gating domain within the deaminase fold regulates the active site sterically and mechanistically in a process that we termed gated zinc shutter. Based on the structures, an autoinhibited ground state and its activation are cross-validated by RNA editing assays and differential scanning fluorimetry. We anticipate that, in vivo, the framework of an active plant RNA editosome triggers the release of DYW autoinhibition to ensure a controlled and coordinated cytidine deamination playing a key role in mitochondrial and chloroplast homeostasis.

PubMed: 34712911
DOI: 10.1038/s41929-021-00633-x

Experimental method

X-RAY DIFFRACTION (1.65 Å)