2J5B

Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Virus-Encoded Aminoacyl-tRNA Synthetases: Structural and Functional Characterization of Mimivirus Tyrrs and Metrs.

Abergel, C.Rudinger-Thirion, J.Giege, R.Claverie, J.M.

(2007) J.Virol. 81: 12406

  • DOI: 10.1128/JVI.01107-07

  • PubMed Abstract: 
  • Aminoacyl-tRNA synthetases are pivotal in determining how the genetic code is translated in amino acids and in providing the substrate for protein synthesis. As such, they fulfill a key role in a process universally conserved in all cellular organism ...

    Aminoacyl-tRNA synthetases are pivotal in determining how the genetic code is translated in amino acids and in providing the substrate for protein synthesis. As such, they fulfill a key role in a process universally conserved in all cellular organisms from their most complex to their most reduced parasitic forms. In contrast, even complex viruses were not found to encode much translation machinery, with the exception of isolated components such as tRNAs. In this context, the discovery of four aminoacyl-tRNA synthetases encoded in the genome of mimivirus together with a full set of translation initiation, elongation, and termination factors appeared to blur what was once a clear frontier between the cellular and viral world. Functional studies of two mimivirus tRNA synthetases confirmed the MetRS specificity for methionine and the TyrRS specificity for tyrosine and conformity with the identity rules for tRNA(Tyr) for archea/eukarya. The atomic structure of the mimivirus tyrosyl-tRNA synthetase in complex with tyrosinol exhibits the typical fold and active-site organization of archaeal-type TyrRS. However, the viral enzyme presents a unique dimeric conformation and significant differences in its anticodon binding site. The present work suggests that mimivirus aminoacyl-tRNA synthetases function as regular translation enzymes in infected amoebas. Their phylogenetic classification does not suggest that they have been acquired recently by horizontal gene transfer from a cellular host but rather militates in favor of an intricate evolutionary relationship between large DNA viruses and ancestral eukaryotes.


    Related Citations: 
    • Mimivirus Tyrrs: Preliminary Structural and Functional Characterization of the First Amino- Acyl tRNA Synthetase Found in a Virus.
      Abergel, C.,Chenivesse, S.,Byrne, D.,Suhre, K.,Arondel, V.,Claverie, J.-M.
      (2005) Acta Crystallogr.,Sect.F 61: 212


    Organizational Affiliation

    Structural and Genomic Information Laboratory, CNRS-UPR2589, IBSM-IFR88, 163 Avenue de Luminy, Case 934, 13288, Marseille Cedex 9, France. Chantal.Abergel@igs.cnrs-mrs.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYROSYL-TRNA SYNTHETASE
A, B
348Acanthamoeba polyphaga mimivirusMutation(s): 0 
Gene Names: YARS
EC: 6.1.1.1
Find proteins for Q5UPJ7 (Acanthamoeba polyphaga mimivirus)
Go to Gene View: YARS
Go to UniProtKB:  Q5UPJ7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYE
Query on TYE

Download SDF File 
Download CCD File 
A, B
4-[(2S)-2-amino-3-hydroxypropyl]phenol
tyrosinol, bound form of TYROSINAL
C9 H13 N O2
DBLDQZASZZMNSL-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.502α = 90.00
b = 107.300β = 90.00
c = 148.890γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-06-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-10-17
    Type: Data collection, Structure summary