6NLY

Fragment of human mitochondrial Alanyl-tRNA Synthetase C-Ala domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Relaxed sequence constraints favor mutational freedom in idiosyncratic metazoan mitochondrial tRNAs.

Kuhle, B.Chihade, J.Schimmel, P.

(2020) Nat Commun 11: 969-969

  • DOI: https://doi.org/10.1038/s41467-020-14725-y
  • Primary Citation of Related Structures:  
    6NLQ, 6NLY, 6NOW

  • PubMed Abstract: 

    Metazoan complexity and life-style depend on the bioenergetic potential of mitochondria. However, higher aerobic activity and genetic drift impose strong mutation pressure and risk of irreversible fitness decline in mitochondrial (mt)DNA-encoded genes. Bilaterian mitochondria-encoded tRNA genes, key players in mitochondrial activity, have accumulated mutations at significantly higher rates than their cytoplasmic counterparts, resulting in foreshortened and fragile structures. Here we show that fragility of mt tRNAs coincided with the evolution of bilaterian animals. We demonstrate that bilaterians compensated for this reduced structural complexity in mt tRNAs by sequence-independent induced-fit adaption to the cognate mitochondrial aminoacyl-tRNA synthetase (aaRS). Structural readout by nuclear-encoded aaRS partners relaxed the sequence constraints on mt tRNAs and facilitated accommodation of functionally disruptive mutational insults by cis-acting epistatic compensations. Our results thus suggest that mutational freedom in mt tRNA genes is an adaptation to increased mutation pressure that was associated with the evolution of animal complexity.


  • Organizational Affiliation

    The Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, CA, 92037, USA. bkuhle@scripps.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alanine--tRNA ligase, mitochondrialA [auth B],
B [auth A],
C,
D
192Homo sapiensMutation(s): 0 
Gene Names: AARS2AARSLKIAA1270
EC: 6.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q5JTZ9 (Homo sapiens)
Explore Q5JTZ9 
Go to UniProtKB:  Q5JTZ9
PHAROS:  Q5JTZ9
GTEx:  ENSG00000124608 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JTZ9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.22α = 90
b = 317.23β = 90
c = 54.71γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Database references, Structure summary
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description