1H4V

HISTIDYL-TRNA SYNTHETASE from Thermus Thermophilus (ligand free)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Succession of Substrate Induced Conformational Changes Ensures the Amino Acid Specificity of Thermus Thermophilus Prolyl-tRNA Synthetase: Comparison with Histidyl-tRNA Synthetase

Yaremchuk, A.Tukalo, M.Grotli, M.Cusack, S.

(2001) J.Mol.Biol. 309: 989

  • DOI: 10.1006/jmbi.2001.4712
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe the recognition by Thermus thermophilus prolyl-tRNA synthetase (ProRSTT) of proline, ATP and prolyl-adenylate and the sequential conformational changes occurring when the substrates bind and the activated intermediate is formed. Proline a ...

    We describe the recognition by Thermus thermophilus prolyl-tRNA synthetase (ProRSTT) of proline, ATP and prolyl-adenylate and the sequential conformational changes occurring when the substrates bind and the activated intermediate is formed. Proline and ATP binding cause respectively conformational changes in the proline binding loop and motif 2 loop. However formation of the activated intermediate is necessary for the final conformational ordering of a ten residue peptide ("ordering loop") close to the active site which would appear to be essential for functional tRNA 3' end binding. These induced fit conformational changes ensure that the enzyme is highly specific for proline activation and aminoacylation. We also present new structures of apo and AMP bound histidyl-tRNA synthetase (HisRS) from T. thermophilus which we compare to our previous structures of the histidine and histidyl-adenylate bound enzyme. Qualitatively, similar results to those observed with T. thermophilus prolyl-tRNA synthetase are found. However histidine binding is sufficient to induce the co-operative ordering of the topologically equivalent histidine binding loop and ordering loop. These two examples contrast with most other class II aminoacyl-tRNA synthetases whose pocket for the cognate amino acid side-chain is largely preformed. T. thermophilus prolyl-tRNA synthetase appears to be the second class II aminoacyl-tRNA synthetase, after HisRS, to use a positively charged amino acid instead of a divalent cation to catalyse the amino acid activation reaction.


    Related Citations: 
    • Crystal Structure Analysis of the Activation of Histidine by Thermus Thermophilus Histidyl-tRNA Synthetase
      Aberg, A.,Yaremchuk, A.,Tukalo, M.,Rasmussen, B.,Cusack, S.
      (1997) Biochemistry 36: 3084


    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
HISTIDYL-TRNA SYNTHETASE
B
421Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: hisS
EC: 6.1.1.21
Find proteins for P62374 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62374
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 111.130α = 90.00
b = 102.150β = 90.00
c = 91.510γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CCP4data scaling
MOSFLMdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance