1IL2

Crystal Structure of the E. coli Aspartyl-tRNA Synthetase:Yeast tRNAasp:aspartyl-Adenylate Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

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Literature

The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism.

Moulinier, L., Eiler, S., Eriani, G., Gangloff, J., Thierry, J.C., Gabriel, K., McClain, W.H., Moras, D.

(2001) EMBO J 20: 5290-5301

  • DOI: https://doi.org/10.1093/emboj/20.18.5290
  • Primary Citation of Related Structures:  
    1IL2

  • PubMed Abstract: 

    • The 2.6 A resolution crystal structure of an inactive complex between yeast tRNA(Asp) and Escherichia coli aspartyl-tRNA synthetase reveals the molecular details of a tRNA-induced mechanism that controls the specificity of the reaction. The dimer is asymmetric, with only one of the two bound tRNAs entering the active site cleft of its subunit ...

    The 2.6 A resolution crystal structure of an inactive complex between yeast tRNA(Asp) and Escherichia coli aspartyl-tRNA synthetase reveals the molecular details of a tRNA-induced mechanism that controls the specificity of the reaction. The dimer is asymmetric, with only one of the two bound tRNAs entering the active site cleft of its subunit. However, the flipping loop, which controls the proper positioning of the amino acid substrate, acts as a lid and prevents the correct positioning of the terminal adenosine. The structure suggests that the acceptor stem regulates the loop movement through sugar phosphate backbone- protein interactions. Solution and cellular studies on mutant tRNAs confirm the crucial role of the tRNA three-dimensional structure versus a specific recognition of bases in the control mechanism.

    Organizational Affiliation: 

    UPR 9004, Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP 163, 67404 Illkirch Cedex, France.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ASPARTYL-TRNA SYNTHETASEC [auth A],
D [auth B]		590Escherichia coliMutation(s): 0 
EC: 6.1.1.12
UniProt
Find proteins for P21889 (Escherichia coli (strain K12))
Explore P21889 
Go to UniProtKB:  P21889
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21889
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
ASPARTYL TRANSFER RNAA [auth C],
B [auth D]		75Saccharomyces cerevisiae
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMO
Query on AMO
Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]		ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE
C14 H19 N6 O10 P
QPBSGQWTJLPZNF-VWJPMABRSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth C],
G [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.8α = 90
b = 222.8β = 111.8
c = 80.8γ = 90
Software Package:
Software NamePurpose
ALMNmodel building
TSFGENmodel building
CNSrefinement
CCP4phasing
TSFGEN)phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Data collection, Database references, Derived calculations