1EFW

Crystal structure of aspartyl-tRNA synthetase from Thermus thermophilus complexed to tRNAasp from Escherichia coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

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This is version 1.2 of the entry. See complete history. 


Literature

An intermediate step in the recognition of tRNA(Asp) by aspartyl-tRNA synthetase.

Briand, C., Poterszman, A., Eiler, S., Webster, G., Thierry, J., Moras, D.

(2000) J Mol Biol 299: 1051-1060

  • DOI: 10.1006/jmbi.2000.3819
  • Primary Citation of Related Structures:  
    1EFW

  • PubMed Abstract: 

    • The crystal structures of aspartyl-tRNA synthetase (AspRS) from Thermus thermophilus, a prokaryotic class IIb enzyme, complexed with tRNA(Asp) from either T. thermophilus or Escherichia coli reveal a potential intermediate of the recognition process. The tRNA is positioned on the enzyme such that it cannot be aminoacylated but adopts an overall conformation similar to that observed in active complexes ...

    The crystal structures of aspartyl-tRNA synthetase (AspRS) from Thermus thermophilus, a prokaryotic class IIb enzyme, complexed with tRNA(Asp) from either T. thermophilus or Escherichia coli reveal a potential intermediate of the recognition process. The tRNA is positioned on the enzyme such that it cannot be aminoacylated but adopts an overall conformation similar to that observed in active complexes. While the anticodon loop binds to the N-terminal domain of the enzyme in a manner similar to that of the related active complexes, its aminoacyl acceptor arm remains at the entrance of the active site, stabilized in its intermediate conformational state by non-specific interactions with the insertion and catalytic domains. The thermophilic nature of the enzyme, which manifests itself in a very low kinetic efficiency at 17 degrees C, the temperature at which the crystals were grown, is in agreement with the relative stability of this non-productive conformational state. Based on these data, a pathway for tRNA binding and recognition is proposed.

    Organizational Affiliation: 

    IGBMC CNRS/INSERM/ULP, UPR 9004, Laboratoire de Biologie et Génomique Structurale, 1, rue Laurent Fries, Illkirch Cedex, C.U. de Strasbourg, B.P. 163, France.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ASPARTYL-TRNA SYNTHETASEC [auth A],
D [auth B]		580Thermus thermophilusMutation(s): 0 
Gene Names: aspS
EC: 6.1.1.12
UniProt
Find proteins for P36419 (Thermus thermophilus)
Explore P36419 
Go to UniProtKB:  P36419
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36419
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
ASPARTYL-TRNAA [auth C],
B [auth D]		73Escherichia coli
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 251.45α = 90
b = 251.45β = 90
c = 88.7γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance