1C0A

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.249 
  • R-Value Work: 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

  • 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 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 TRNAB77Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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

Download SDF File 
Download CCD File 
A
ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE
C14 H19 N6 O10 P
QPBSGQWTJLPZNF-VWJPMABRSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
B
RNA LINKINGC9 H13 N2 O9 PU
4SU
Query on 4SU
B
RNA LINKINGC9 H13 N2 O8 P SU
G7M
Query on G7M
B
RNA LINKINGC11 H17 N5 O8 PG
QUO
Query on QUO
B
RNA LINKINGC17 H26 N5 O10 PG
5MU
Query on 5MU
B
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
B
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.200α = 90.00
b = 101.200β = 90.00
c = 231.810γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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