5MGV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1002/pro.3176
  • Primary Citation of Related Structures:  

  • 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 recogn ...

    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

    Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Structural Biology, Weizmann Institute of Science, Israel.,Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.,Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle, NE2 4HH, United Kingdom.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore.,Ambry Genetics, California.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylalanine--tRNA ligase, mitochondrial
A
405Homo sapiensMutation(s): 1 
Gene Names: FARS2 (FARS1)
EC: 6.1.1.20
Find proteins for O95363 (Homo sapiens)
Go to Gene View: FARS2
Go to UniProtKB:  O95363
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.770α = 90.00
b = 90.370β = 90.00
c = 95.170γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Database references
  • Version 1.2: 2018-10-24
    Type: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-10-16
    Type: Data collection