5XAQ

Crystal structure of Animalia-specific tRNA deacylase from Mus musculus

Summary for 5XAQ

• Entry DOI: 10.2210/pdb5xaq/pdb
• Descriptor: Probable D-tyrosyl-tRNA(Tyr) deacylase 2 (2 entities in total)
• Functional Keywords: trna, deacylase, hydrolase
• Biological source: Mus musculus (Mouse)
• Cellular location: Cytoplasm : Q8BHA3
• Total number of polymer chains: 2
• Total formula weight: 36517.67

Authors

Kuncha, K.S.,Kattula, B.,Sankarnarayanan, R. (deposition date: 2017-03-14, release date: 2018-02-14, Last modification date: 2023-11-22)

Primary citation

Kuncha, S.K.,Mazeed, M.,Singh, R.,Kattula, B.,Routh, S.B.,Sankaranarayanan, R.
A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia
Nat Commun, 9:511-511, 2018

PubMed Abstract: D-aminoacyl-tRNA deacylase (DTD), a bacterial/eukaryotic trans-editing factor, removes D-amino acids mischarged on tRNAs and achiral glycine mischarged on tRNA. An invariant cross-subunit Gly-cisPro motif forms the mechanistic basis of L-amino acid rejection from the catalytic site. Here, we present the identification of a DTD variant, named ATD (Animalia-specific tRNA deacylase), that harbors a Gly-transPro motif. The cis-to-trans switch causes a "gain of function" through L-chiral selectivity in ATD resulting in the clearing of L-alanine mischarged on tRNA(G4•U69) by eukaryotic AlaRS. The proofreading activity of ATD is conserved across diverse classes of phylum Chordata. Animalia genomes enriched in tRNA(G4•U69) genes are in strict association with the presence of ATD, underlining the mandatory requirement of a dedicated factor to proofread tRNA misaminoacylation. The study highlights the emergence of ATD during genome expansion as a key event associated with the evolution of Animalia.

PubMed: 29410408
DOI: 10.1038/s41467-017-02204-w

Experimental method

X-RAY DIFFRACTION (1.86 Å)