2PID

Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Human Mitochondrial Tyrosyl-tRNA Synthetase Reveals Common and Idiosyncratic Features.

Bonnefond, L.Frugier, M.Touze, E.Lorber, B.Florentz, C.Giege, R.Sauter, C.Rudinger-Thirion, J.

(2007) Structure 15: 1505-1516

  • DOI: 10.1016/j.str.2007.09.018
  • Primary Citation of Related Structures:  
    2PID

  • PubMed Abstract: 
  • We report the structure of a strictly mitochondrial human synthetase, namely tyrosyl-tRNA synthetase (mt-TyrRS), in complex with an adenylate analog at 2.2 A resolution. The structure is that of an active enzyme deprived of the C-terminal S4-like domain ...

    We report the structure of a strictly mitochondrial human synthetase, namely tyrosyl-tRNA synthetase (mt-TyrRS), in complex with an adenylate analog at 2.2 A resolution. The structure is that of an active enzyme deprived of the C-terminal S4-like domain and resembles eubacterial TyrRSs with a canonical tyrosine-binding pocket and adenylate-binding residues typical of class I synthetases. Two bulges at the enzyme surface, not seen in eubacterial TyrRSs, correspond to conserved sequences in mt-TyrRSs. The synthetase electrostatic surface potential differs from that of other TyrRSs, including the human cytoplasmic homolog and the mitochondrial one from Neurospora crassa. The homodimeric human mt-TyrRS shows an asymmetry propagating from the dimer interface toward the two catalytic sites and extremities of each subunit. Mutagenesis of the catalytic domain reveals functional importance of Ser200 in line with an involvement of A73 rather than N1-N72 in tyrosine identity.


    Related Citations: 
    • Tyrosyl-tRNA synthetase: the first crystallization of a human mitochondrial aminoacyl-tRNA synthetase
      Bonnefond, L., Frugier, M., Touze, E., Lorber, B., Florentz, C., Giege, R., Rudinger-Thirion, J., Sauter, C.
      (2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 338

    Organizational Affiliation

    Département Machineries Traductionnelles, Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosyl-tRNA synthetase AB356Homo sapiensMutation(s): 0 
Gene Names: YARS2CGI-04
EC: 6.1.1.1
Find proteins for Q9Y2Z4 (Homo sapiens)
Explore Q9Y2Z4 
Go to UniProtKB:  Q9Y2Z4
NIH Common Fund Data Resources
PHAROS:  Q9Y2Z4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YSA
Query on YSA

Download Ideal Coordinates CCD File 
A, B
5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE
C19 H23 N7 O8 S
MJZAZMKENKZBAJ-QTOWJTHWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54α = 90
b = 62.4β = 90
c = 194.6γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance