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: 2.90 Å
  • R-Value Free: 
    0.269 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ATPClick on this verticalbar to view detailsBest fitted TYEClick on this verticalbar to view details

This is version 1.5 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: https://doi.org/10.1093/emboj/cdf373
  • Primary Citation of Related Structures:  
    1H3E, 1H3F

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TYROSYL-TRNA SYNTHETASE432Thermus thermophilus HB27Mutation(s): 0 
EC: 6.1.1.1
UniProt
Find proteins for P83453 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore P83453 
Go to UniProtKB:  P83453
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83453
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
TYE
Query on TYE

Download Ideal Coordinates CCD File 
D [auth A]4-[(2S)-2-amino-3-hydroxypropyl]phenol
C9 H13 N O2
DBLDQZASZZMNSL-QMMMGPOBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.269 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.525α = 90
b = 129.525β = 90
c = 109.451γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ATPClick on this verticalbar to view detailsBest fitted TYEClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-27
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2015-08-19
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 1.3: 2018-10-17
    Changes: Data collection, Structure summary
  • Version 1.4: 2019-10-30
    Changes: Data collection, Derived calculations, Other
  • Version 1.5: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary