5THH

Crystal structure of a human tyrosyl-tRNA synthetase mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1093/nar/gkx455
  • Primary Citation of Related Structures:  
    5THH, 5THL

  • 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 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

    Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine--tRNA ligase, cytoplasmic339Homo sapiensMutation(s): 1 
Gene Names: YARS
EC: 6.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54577 (Homo sapiens)
Explore P54577 
Go to UniProtKB:  P54577
PHAROS:  P54577
GTEx:  ENSG00000134684 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54577
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TYR
Query on TYR

Download Ideal Coordinates CCD File 
B [auth A]TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.238α = 90
b = 75.705β = 90
c = 163.51γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description