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

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis.

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.

(2021) Nat Catal 4: 510-522

  • DOI: https://doi.org/10.1038/s41929-021-00633-x
  • Primary Citation of Related Structures:  
    7O4E, 7O4F

  • 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.

  • Organizational Affiliation

    Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
A, B
138Arabidopsis thalianaMutation(s): 0 
Gene Names: PCMP-H83OTP86At3g63370F16M2_220
Find proteins for Q9M1V3 (Arabidopsis thaliana)
Explore Q9M1V3 
Go to UniProtKB:  Q9M1V3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M1V3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.57α = 90
b = 30.58β = 125.75
c = 77.53γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Data collection, Database references