6O76

Human cytosolic Histidyl-tRNA synthetase (HisRS) with WHEP domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.787 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 4X5O - determined by Kim, Y.K., Jeon, Y.H.  

Literature

CMT disease severity correlates with mutation-induced open conformation of histidyl-tRNA synthetase, not aminoacylation loss, in patient cells.

Blocquel, D.Sun, L.Matuszek, Z.Li, S.Weber, T.Kuhle, B.Kooi, G.Wei, N.Baets, J.Pan, T.Schimmel, P.Yang, X.L.

(2019) Proc.Natl.Acad.Sci.USA 116: 19440-19448

  • DOI: 10.1073/pnas.1908288116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aminoacyl-transfer RNA (tRNA) synthetases (aaRSs) are the largest protein family causatively linked to neurodegenerative Charcot-Marie-Tooth (CMT) disease. Dominant mutations cause the disease, and studies of CMT disease-causing mutant glycyl-tRNA sy ...

    Aminoacyl-transfer RNA (tRNA) synthetases (aaRSs) are the largest protein family causatively linked to neurodegenerative Charcot-Marie-Tooth (CMT) disease. Dominant mutations cause the disease, and studies of CMT disease-causing mutant glycyl-tRNA synthetase (GlyRS) and tyrosyl-tRNA synthetase (TyrRS) showed their mutations create neomorphic structures consistent with a gain-of-function mechanism. In contrast, based on a haploid yeast model, loss of aminoacylation function was reported for CMT disease mutants in histidyl-tRNA synthetase (HisRS). However, neither that nor prior work of any CMT disease-causing aaRS investigated the aminoacylation status of tRNAs in the cellular milieu of actual patients. Using an assay that interrogated aminoacylation levels in patient cells, we investigated a HisRS-linked CMT disease family with the most severe disease phenotype. Strikingly, no difference in charged tRNA levels between normal and diseased family members was found. In confirmation, recombinant versions of 4 other HisRS CMT disease-causing mutants showed no correlation between activity loss in vitro and severity of phenotype in vivo. Indeed, a mutation having the most detrimental impact on activity was associated with a mild disease phenotype. In further work, using 3 independent biophysical analyses, structural opening (relaxation) of mutant HisRSs at the dimer interface best correlated with disease severity. In fact, the HisRS mutation in the severely afflicted patient family caused the largest degree of structural relaxation. These data suggest that HisRS-linked CMT disease arises from open conformation-induced mechanisms distinct from loss of aminoacylation.


    Related Citations: 
    • Structural characteristics of human histidyl-tRNA synthetase
      Kim, Y.K.,Chang, J.E.,Kim, S.,Jeon, Y.H.
      (2014) Biodesign 2: 142
    • Neurodegenerative Charcot-Marie-Tooth disease as a case study to decipher novel functions of aminoacyl-tRNA synthetases.
      Wei, N.,Zhang, Q.,Yang, X.L.
      (2019) J. Biol. Chem. 294: 5321


    Organizational Affiliation

    Neurogenetics Group and Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium.,Dynamic Biosensors GmbH, 82152 Martinsried, Germany.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037; schimmel@scripps.edu xlyang@scripps.edu.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037.,Department of Medicine, University of California San Diego, La Jolla, CA 92037.,School of Public Health (Shenzhen), Sun Yat-sen University, 518107 Guangdong, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histidine--tRNA ligase, cytoplasmic
A, B
509Homo sapiensMutation(s): 0 
Gene Names: HARS (HRS)
EC: 6.1.1.21
Find proteins for P12081 (Homo sapiens)
Go to Gene View: HARS
Go to UniProtKB:  P12081
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.787 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.236 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 97.669α = 90.00
b = 97.669β = 90.00
c = 254.409γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-03-07 
  • Released Date: 2019-09-11 
  • Deposition Author(s): Kuhle, B., Yang, X.L.

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-09-25
    Type: Data collection, Database references
  • Version 1.2: 2019-10-09
    Type: Data collection, Database references