1G51

ASPARTYL TRNA SYNTHETASE FROM THERMUS THERMOPHILUS AT 2.4 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase.

Poterszman, A.Delarue, M.Thierry, J.C.Moras, D.

(1994) J.Mol.Biol. 244: 158-167

  • DOI: 10.1006/jmbi.1994.1716

  • PubMed Abstract: 
  • The crystal structures of Thermus thermophilus aspartyl-tRNA synthetase and of its complex with ATP, Mg2+ and aspartic acid, show in situ formation of the amino acid adenylate and furnish experimental evidence for the modes of recognition of aspartic ...

    The crystal structures of Thermus thermophilus aspartyl-tRNA synthetase and of its complex with ATP, Mg2+ and aspartic acid, show in situ formation of the amino acid adenylate and furnish experimental evidence for the modes of recognition of aspartic acid and ATP. The amino acid fits in a predefined specific site in which it replaces water molecules without significant conformational changes of the binding residues. This mode of selection is reminiscent of the lock and key concept. The pocket is closed by the movement of a histidine side chain from a neighbouring loop acting as a valve. ATP binding is driven by the stacking of the adenine upon the otherwise fixed aromatic ring of the class-II-invariant phenylalanine Phe235. Specific recognition is achieved by interactions with the flexible side chains of other class-II-conserved residues. Conformational changes have been identified which allow the description of a reaction pathway including both lock-and-key and induced-fit interactions. This pathway can presumably be extended to all class II aaRS.


    Organizational Affiliation

    Laboratoire de Biologie Structurale, I.B.M.C. du C.N.R.S., Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.135α = 90.00
b = 155.500β = 90.00
c = 171.145γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
AUTOMARdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description