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 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


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

  • 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 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ASPARTYL-TRNA SYNTHETASE
A, B
580Thermus thermophilusGene Names: aspS
EC: 6.1.1.12
Find proteins for P36419 (Thermus thermophilus)
Go to UniProtKB:  P36419
Entity ID: 1
MoleculeChainsLengthOrganism
ASPARTYL-TRNAC,D73Escherichia coli
Small Molecules
Modified Residues  7 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
C, D
RNA LINKINGC9 H13 N2 O9 PU
4SU
Query on 4SU
C, D
RNA LINKINGC9 H13 N2 O8 P SU
G7M
Query on G7M
C, D
RNA LINKINGC11 H17 N5 O8 PG
QUO
Query on QUO
C, D
RNA LINKINGC17 H26 N5 O10 PG
5MU
Query on 5MU
C, D
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
C, D
RNA LINKINGC11 H16 N5 O7 PA
H2U
Query on H2U
C, D
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.248 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 251.450α = 90.00
b = 251.450β = 90.00
c = 88.700γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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