1H4S

Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG) and a prolyl-adenylate analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 

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 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
    • TRNA(Pro) Recognition by Thermus Thermophilus Prolyl-tRNA Synthetase
      Cusack, S.,Yaremchuk, A.,Krikliviy, I.,Tukalo, M.
      (1997) Structure 6: 101
    • 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.,Sect.D 56: 197
    • Crystallisation and Preliminary X-Ray Diffraction Analysis of Thermus Thermophilus Prolyl-tRNA Synthetase
      Yaremchuk, A.,Cusack, S.,Tukalo, M.
      (2000) Acta Crystallogr.,Sect.D 56: 195


    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
PROLYL-TRNA SYNTHETASE
A, B
477Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: proS
EC: 6.1.1.15
Find proteins for Q5SM28 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SM28
Entity ID: 2
MoleculeChainsLengthOrganism
TRNAPRO(CGG)T77Thermus thermophilus
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PSD
Query on PSD

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Download CCD File 
A, B
5'-O-[N-(PROLYL)-SULFAMOYL]ADENOSINE
C15 H22 N7 O7 P
BIVNOVXAWQKFMF-JVEUSOJLSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
T
RNA LINKINGC9 H13 N2 O9 PU
5MU
Query on 5MU
T
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 140.780α = 90.00
b = 140.780β = 90.00
c = 236.970γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
CNSrefinement
SCALAdata scaling

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