5XAQ | pdb_00005xaq

Crystal structure of Animalia-specific tRNA deacylase from Mus musculus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia

Kuncha, S.K., Mazeed, M., Singh, R., Kattula, B., Routh, S.B., Sankaranarayanan, R.

(2018) Nat Commun 9: 511-511

  • DOI: https://doi.org/10.1038/s41467-017-02204-w
  • Primary Citation Related Structures: 
    5XAQ

  • 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 Ala . 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 Thr (G4•U69) by eukaryotic AlaRS. The proofreading activity of ATD is conserved across diverse classes of phylum Chordata. Animalia genomes enriched in tRNA Thr (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.

    • Organizational Affiliation: 
    • CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.

Macromolecule Content 

  • Total Structure Weight: 36.52 kDa 
  • Atom Count: 2,719 
  • Modeled Residue Count: 327 
  • Deposited Residue Count: 336 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable D-tyrosyl-tRNA(Tyr) deacylase 2
A, B
168Mus musculusMutation(s): 0 
Gene Names: Dtd2
EC: 3.1 (PDB Primary Data), 3.1.1.96 (UniProt)
UniProt
Find proteins for Q8BHA3 (Mus musculus)
Explore Q8BHA3 
Go to UniProtKB:  Q8BHA3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BHA3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.379α = 90
b = 75.351β = 90
c = 103.619γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
AUTOMARdata collection
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
AUTOMARphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
India--

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description