4AH6

Human mitochondrial aspartyl-tRNA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Thermodynamic Properties Distinguish Human Mitochondrial Aspartyl-tRNA Synthetase from Bacterial Homolog with Same 3D Architecture

Ennifar, E.Florentz, C.Gaudry, A.Lorber, B.Neuenfeldt, A.Sauter, C.Sissler, M.

(2013) Nucleic Acids Res. 41: 2698

  • DOI: 10.1093/nar/gks1322

  • PubMed Abstract: 
  • In the mammalian mitochondrial translation apparatus, the proteins and their partner RNAs are coded by two genomes. The proteins are nuclear-encoded and resemble their homologs, whereas the RNAs coming from the rapidly evolving mitochondrial genome h ...

    In the mammalian mitochondrial translation apparatus, the proteins and their partner RNAs are coded by two genomes. The proteins are nuclear-encoded and resemble their homologs, whereas the RNAs coming from the rapidly evolving mitochondrial genome have lost critical structural information. This raises the question of molecular adaptation of these proteins to their peculiar partner RNAs. The crystal structure of the homodimeric bacterial-type human mitochondrial aspartyl-tRNA synthetase (DRS) confirmed a 3D architecture close to that of Escherichia coli DRS. However, the mitochondrial enzyme distinguishes by an enlarged catalytic groove, a more electropositive surface potential and an alternate interaction network at the subunits interface. It also presented a thermal stability reduced by as much as 12°C. Isothermal titration calorimetry analyses revealed that the affinity of the mitochondrial enzyme for cognate and non-cognate tRNAs is one order of magnitude higher, but with different enthalpy and entropy contributions. They further indicated that both enzymes bind an adenylate analog by a cooperative allosteric mechanism with different thermodynamic contributions. The larger flexibility of the mitochondrial synthetase with respect to the bacterial enzyme, in combination with a preserved architecture, may represent an evolutionary process, allowing nuclear-encoded proteins to cooperate with degenerated organelle RNAs.


    Related Citations: 
    • Peculiar Inhibition of Human Mitochondrial Aspartyl-tRNA Synthetase by Adenylate Analogs.
      Messmer, M.,Blais, S.P.,Balg, C.,Chenevert, R.,Grenier, L.,Lague, P.,Sauter, C.,Sissler, M.,Giege, R.,Lapointe, J.,Florentz, C.
      (2009) Biochimie 91: 596
    • Loss of a Primordial Identity Element for a Mammalian Mitochondrial Aminoacylation System.
      Fender, A.,Sauter, C.,Messmer, M.,Putz, J.,Giege, R.,Florentz, C.,Sissler, M.
      (2006) J.Biol.Chem. 281: 15980


    Organizational Affiliation

    Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, F-67084 Strasbourg Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ASPARTATE--TRNA LIGASE, MITOCHONDRIAL
A, B, C, D
617Homo sapiensGene Names: DARS2
EC: 6.1.1.12
Find proteins for Q6PI48 (Homo sapiens)
Go to Gene View: DARS2
Go to UniProtKB:  Q6PI48
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.219 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.400α = 90.00
b = 82.600β = 100.40
c = 146.300γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references