Kinetic and Structural Changes in HsmtPheRS, Induced by Pathogenic Mutations in Human FARS2

Experimental Data Snapshot

  • Resolution: 1.46 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

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Kinetic and structural changes in HsmtPheRS, induced by pathogenic mutations in human FARS2.

Kartvelishvili, E.Tworowski, D.Vernon, H.Moor, N.Wang, J.Wong, L.J.Chrzanowska-Lightowlers, Z.Safro, M.

(2017) Protein Sci 26: 1505-1516

  • DOI: https://doi.org/10.1002/pro.3176
  • Primary Citation of Related Structures:  
    5MGH, 5MGU, 5MGV, 5MGW

  • PubMed Abstract: 

    Mutations in the mitochondrial aminoacyl-tRNA synthetases (mtaaRSs) can cause profound clinical presentations, and have manifested as diseases with very selective tissue specificity. To date most of the mtaaRS mutations could be phenotypically recognized, such that clinicians could identify the affected mtaaRS from the symptoms alone. Among the recently reported pathogenic variants are point mutations in FARS2 gene, encoding the human mitochondrial PheRS. Patient symptoms range from spastic paraplegia to fatal infantile Alpers encephalopathy. How clinical manifestations of these mutations relate to the changes in three-dimensional structures and kinetic characteristics remains unclear, although impaired aminoacylation has been proposed as possible etiology of diseases. Here, we report four crystal structures of HsmtPheRS mutants, and extensive MD simulations for wild-type and nine mutants to reveal the structural changes on dynamic trajectories of HsmtPheRS. Using steady-state kinetic measurements of phenylalanine activation and tRNA Phe aminoacylation, we gained insight into the structural and kinetic effects of mitochondrial disease-related mutations in FARS2 gene.

  • Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylalanine--tRNA ligase, mitochondrial406Homo sapiensMutation(s): 1 
Gene Names: FARS2FARS1HSPC320
UniProt & NIH Common Fund Data Resources
Find proteins for O95363 (Homo sapiens)
Explore O95363 
Go to UniProtKB:  O95363
PHAROS:  O95363
GTEx:  ENSG00000145982 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95363
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PHE

Download Ideal Coordinates CCD File 
C9 H11 N O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.46 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.355α = 90
b = 90.117β = 90
c = 99.081γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references