1C0A

CRYSTAL STRUCTURE OF THE E. COLI ASPARTYL-TRNA SYNTHETASE : TRNAASP : ASPARTYL-ADENYLATE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step.

Eiler, S.Dock-Bregeon, A.Moulinier, L.Thierry, J.C.Moras, D.

(1999) EMBO J 18: 6532-6541

  • DOI: 10.1093/emboj/18.22.6532
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The 2.4 A crystal structure of the Escherichia coli aspartyl-tRNA synthetase (AspRS)-tRNA(Asp)-aspartyl-adenylate complex shows the two substrates poised for the transfer of the aspartic acid moiety from the adenylate to the 3'-hydroxyl of the termin ...

    The 2.4 A crystal structure of the Escherichia coli aspartyl-tRNA synthetase (AspRS)-tRNA(Asp)-aspartyl-adenylate complex shows the two substrates poised for the transfer of the aspartic acid moiety from the adenylate to the 3'-hydroxyl of the terminal adenosine of the tRNA. A general molecular mechanism is proposed for the second step of the aspartylation reaction that accounts for the observed conformational changes, notably in the active site pocket. The stabilization of the transition state is mediated essentially by two amino acids: the class II invariant arginine of motif 2 and the eubacterial-specific Gln231, which in eukaryotes and archaea is replaced by a structurally non-homologous serine. Two archetypal RNA-protein modes of interactions are observed: the anticodon stem-loop, including the wobble base Q, binds to the N-terminal beta-barrel domain through direct protein-RNA interactions, while the binding of the acceptor stem involves both direct and water-mediated hydrogen bonds in an original recognition scheme.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ASPARTYL TRNA SYNTHETASE
A
585Escherichia coliMutation(s): 0 
EC: 6.1.1.12
Find proteins for P21889 (Escherichia coli (strain K12))
Go to UniProtKB:  P21889
Protein Feature View
  • Reference Sequence

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
ASPARTYL TRNAB77Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMO
Query on AMO

Download CCD File 
A
ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE
C14 H19 N6 O10 P
QPBSGQWTJLPZNF-VWJPMABRSA-N
 Ligand Interaction
AMP
Query on AMP

Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.2α = 90
b = 101.2β = 90
c = 231.81γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance