1IL2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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: 10.1093/emboj/20.18.5290

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ASPARTYL-TRNA SYNTHETASE
A, B
590Escherichia coli (strain K12)Gene Names: aspS (tls)
EC: 6.1.1.12
Find proteins for P21889 (Escherichia coli (strain K12))
Go to UniProtKB:  P21889
Entity ID: 1
MoleculeChainsLengthOrganism
ASPARTYL TRANSFER RNAC,D75Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
AMO
Query on AMO

Download SDF File 
Download CCD File 
A, B
ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE
C14 H19 N6 O10 P
QPBSGQWTJLPZNF-VWJPMABRSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
C, D
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
C, D
RNA LINKINGC10 H16 N3 O8 PC
1MG
Query on 1MG
C, D
RNA LINKINGC11 H16 N5 O8 PG
5MU
Query on 5MU
C, D
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
C, D
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.800α = 90.00
b = 222.800β = 111.80
c = 80.800γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
TSFGEN)phasing
TSFGENmodel building
ALMNmodel building
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance