1HC7

Prolyl-tRNA synthetase from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

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:  
    1H4T, 1H4S, 1H4Q, 1H4V, 1HC7

  • 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 of a Eukaryote/Archaeon-Like Prolyl-tRNA Synthetase and its Complex with tRNA (Pro)(Cgg)
      Yaremchuk, A., Cusack, S., Tukalo, M.
      (2000) EMBO J 19: 4745
    • Crystallisation and Preliminary X-Ray Diffraction Analysis of Thermus Thermophilus Prolyl-tRNA Synthetase
      Yaremchuk, A., Cusack, S., Tukalo, M.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 195
    • Improved Crystals of Thermus Thermophilus Prolyl-tRNA Synthetase Complexed with Cognate tRNA Obtained by Crystallisation from Precipitate
      Yaremchuk, A., Krikliviy, I., Cusack, S., Tukalo, M.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 197
    • TRNA(Pro) Recognition by Thermus Thermophilus Prolyl-tRNA Synthetase
      Cusack, S., Yaremchuk, A., Krikliviy, I., Tukalo, M.
      (1997) Structure 6: 101

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROLYL-TRNA SYNTHETASEABCD477Thermus thermophilusMutation(s): 0 
EC: 6.1.1.15
Find proteins for Q5SM28 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SM28 
Go to UniProtKB:  Q5SM28
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.3α = 90
b = 191.1β = 90
c = 125.1γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RSPSphasing
MLPHAREphasing
DMphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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