8AW3

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

Summary for 8AW3

• Entry DOI: 10.2210/pdb8aw3/pdb
• EMDB information: 15690
• Descriptor: RNA (75-MER), Deaminase, putative, ZINC ION, ... (4 entities in total)
• Functional Keywords: adat; inosine; trna modification; deaminase; cryo-em structure; trypanosoma brucei, rna binding protein
• Biological source: Trypanosoma brucei brucei; More
• Total number of polymer chains: 3
• Total formula weight: 88410.92

Authors

Dolce, L.G.,Tengo, L.,Weis, F.,Kowalinski, E. (deposition date: 2022-08-29, release date: 2022-11-16, Last modification date: 2025-07-02)

Primary citation

Dolce, L.G.,Zimmer, A.A.,Tengo, L.,Weis, F.,Rubio, M.A.T.,Alfonzo, J.D.,Kowalinski, E.
Structural basis for sequence-independent substrate selection by eukaryotic wobble base tRNA deaminase ADAT2/3.
Nat Commun, 13:6737-6737, 2022

PubMed Abstract: The essential deamination of adenosine A 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 deamination evolved, shaped the genetic code, and directly impacts the eukaryotic proteome.

PubMed: 36347890
DOI: 10.1038/s41467-022-34441-z

Experimental method

ELECTRON MICROSCOPY (3.6 Å)