1H3E

Tyrosyl-tRNA synthetase from Thermus thermophilus complexed with wild-type tRNAtyr(GUA) and with ATP and tyrosinol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Class I Tyrosyl-tRNA Synthetase Has a Class II Mode or tRNA Recognition

Yaremchuk, A.Kriklivyi, I.Tukalo, M.Cusack, S.

(2002) Embo J. 21: 3829

  • DOI: 10.1093/emboj/cdf373
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial tyrosyl-tRNA synthetases (TyrRS) possess a flexibly linked C-terminal domain of approximately 80 residues, which has hitherto been disordered in crystal structures of the enzyme. We have determined the structure of Thermus thermophilus TyrR ...

    Bacterial tyrosyl-tRNA synthetases (TyrRS) possess a flexibly linked C-terminal domain of approximately 80 residues, which has hitherto been disordered in crystal structures of the enzyme. We have determined the structure of Thermus thermophilus TyrRS at 2.0 A resolution in a crystal form in which the C-terminal domain is ordered, and confirm that the fold is similar to part of the C-terminal domain of ribosomal protein S4. We have also determined the structure at 2.9 A resolution of the complex of T.thermophilus TyrRS with cognate tRNA(tyr)(G Psi A). In this structure, the C-terminal domain binds between the characteristic long variable arm of the tRNA and the anti-codon stem, thus recognizing the unique shape of the tRNA. The anticodon bases have a novel conformation with A-36 stacked on G-34, and both G-34 and Psi-35 are base-specifically recognized. The tRNA binds across the two subunits of the dimeric enzyme and, remarkably, the mode of recognition of the class I TyrRS for its cognate tRNA resembles that of a class II synthetase in being from the major groove side of the acceptor stem.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, c/o ILL, 156X, F-38042 Grenoble cedex 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYROSYL-TRNA SYNTHETASE
A
432Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: tyrS
EC: 6.1.1.1
Find proteins for P83453 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P83453
Entity ID: 2
MoleculeChainsLengthOrganism
WILD-TYPE TRNATYR(GUA)B86Thermus thermophilus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYE
Query on TYE

Download SDF File 
Download CCD File 
A
4-[(2S)-2-amino-3-hydroxypropyl]phenol
tyrosinol
C9 H13 N O2
DBLDQZASZZMNSL-QMMMGPOBSA-N
 Ligand Interaction
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
B
RNA LINKINGC9 H13 N2 O9 PU
1MA
Query on 1MA
B
RNA LINKINGC11 H16 N5 O7 PA
5MU
Query on 5MU
B
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.219 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 129.525α = 90.00
b = 129.525β = 90.00
c = 109.451γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-27
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2015-08-19
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary