5THH

Crystal structure of a human tyrosyl-tRNA synthetase mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.959 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Alternative stable conformation capable of protein misinteraction links tRNA synthetase to peripheral neuropathy.

Blocquel, D.Li, S.Wei, N.Daub, H.Sajish, M.Erfurth, M.L.Kooi, G.Zhou, J.Bai, G.Schimmel, P.Jordanova, A.Yang, X.L.

(2017) Nucleic Acids Res. 45: 8091-8104

  • DOI: 10.1093/nar/gkx455
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • While having multiple aminoacyl-tRNA synthetases implicated in Charcot-Marie-Tooth (CMT) disease suggests a common mechanism, a defect in enzymatic activity is not shared among the CMT-causing mutants. Protein misfolding is a common hypothesis underl ...

    While having multiple aminoacyl-tRNA synthetases implicated in Charcot-Marie-Tooth (CMT) disease suggests a common mechanism, a defect in enzymatic activity is not shared among the CMT-causing mutants. Protein misfolding is a common hypothesis underlying the development of many neurological diseases. Its process usually involves an initial reduction in protein stability and then the subsequent oligomerization and aggregation. Here, we study the structural effect of three CMT-causing mutations in tyrosyl-tRNA synthetase (TyrRS or YARS). Through various approaches, we found that the mutations do not induce changes in protein secondary structures, or shared effects on oligomerization state and stability. However, all mutations provide access to a surface masked in the wild-type enzyme, and that access correlates with protein misinteraction. With recent data on another CMT-linked tRNA synthetase, we suggest that an inherent plasticity, engendering the formation of alternative stable conformations capable of aberrant interactions, links the tRNA synthetase family to CMT.


    Organizational Affiliation

    Dynamic Biosensors GmbH, 82152 Martinsried, Germany.,Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.,Molecular Neurogenomics Group, VIB Center for Molecular Neurology, University of Antwerp, 2610 Antwerpen, Belgium.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine--tRNA ligase, cytoplasmic
A
339Homo sapiensMutation(s): 1 
Gene Names: YARS
EC: 6.1.1.1
Find proteins for P54577 (Homo sapiens)
Go to Gene View: YARS
Go to UniProtKB:  P54577
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYR
Query on TYR

Download SDF File 
Download CCD File 
A
TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.959 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.238α = 90.00
b = 75.705β = 90.00
c = 163.510γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Database references