8AW3

Cryo-EM structure of the Tb ADAT2/3 deaminase in complex with tRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for sequence-independent substrate selection by eukaryotic wobble base tRNA deaminase ADAT2/3.

Dolce, L.G.Zimmer, A.A.Tengo, L.Weis, F.Rubio, M.A.T.Alfonzo, J.D.Kowalinski, E.

(2022) Nat Commun 13: 6737-6737

  • DOI: https://doi.org/10.1038/s41467-022-34441-z
  • Primary Citation of Related Structures:  
    8AW3

  • PubMed Abstract: 

    The essential deamination of adenosine A 34 to inosine at the wobble base is the individual tRNA modification with the greatest effects on mRNA decoding, empowering a single tRNA to translate three different codons. To date, many aspects of how eukaryotic deaminases specifically select their multiple substrates remain unclear. Here, using cryo-EM, we present the structure of a eukaryotic ADAT2/3 deaminase bound to a full-length tRNA, revealing that the enzyme distorts the anticodon loop, but in contrast to the bacterial enzymes, selects its substrate via sequence-independent contacts of eukaryote-acquired flexible or intrinsically unfolded motifs distal from the conserved catalytic core. A gating mechanism for substrate entry to the active site is identified. Our multi-step tRNA recognition model yields insights into how RNA editing by A 34 deamination evolved, shaped the genetic code, and directly impacts the eukaryotic proteome.


  • Organizational Affiliation

    EMBL Grenoble, 71 Avenue des Martyrs, 38042, Grenoble, France.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Deaminase, putativeB [auth 2]221Trypanosoma brucei bruceiMutation(s): 2 
Gene Names: Tb08.29H22.100Tb927.8.4180
EC: 3.5.4
UniProt
Find proteins for Q57W17 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57W17 
Go to UniProtKB:  Q57W17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57W17
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Deaminase, putativeC [auth 3]369Trypanosoma brucei bruceiMutation(s): 4 
Gene Names: Tb11.01.6930
EC: 3.5.4.33
UniProt
Find proteins for Q381Q7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q381Q7 
Go to UniProtKB:  Q381Q7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ381Q7
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (75-MER)A [auth 1]75Trypanosoma brucei
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-20-CE11-0016

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Structure summary
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references