1ZQ1

Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for tRNA-Dependent Amidotransferase Function

Schmitt, E.Panvert, M.Blanquet, S.Mechulam, Y.

(2005) Structure 13: 1421-1433

  • DOI: 10.1016/j.str.2005.06.016

  • PubMed Abstract: 
  • Besides direct charging of tRNAs by aminoacyl-tRNA synthetases, indirect routes also ensure attachment of some amino acids onto tRNA. Such routes may explain how new amino acids entered into protein synthesis. In archaea and in most bacteria, tRNA(Gl ...

    Besides direct charging of tRNAs by aminoacyl-tRNA synthetases, indirect routes also ensure attachment of some amino acids onto tRNA. Such routes may explain how new amino acids entered into protein synthesis. In archaea and in most bacteria, tRNA(Gln) is first misaminoacylated by glutamyl-tRNA synthetase. Glu-tRNA(Gln) is then matured into Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. We report the structure of a tRNA-dependent amidotransferase-that of GatDE from Pyrococcus abyssi. The 3.0 A resolution crystal structure shows a tetramer with two GatD molecules as the core and two GatE molecules at the periphery. The fold of GatE cannot be related to that of any tRNA binding enzyme. The ammonium donor site on GatD and the tRNA site on GatE are markedly distant. Comparison of GatD and L-asparaginase structures shows how the motion of a beta hairpin region containing a crucial catalytic threonine may control the overall reaction cycle of GatDE.


    Organizational Affiliation

    Laboratoire de Biochimie, Unité Mixte de Recherche 7654, CNRS-Ecole Polytechnique, F-91128 Palaiseau cedex, France. emma@botrytis.polytechnique.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamyl-tRNA(Gln) amidotransferase subunit D
A, B
438Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 0 
Gene Names: gatD
EC: 6.3.5.-
Find proteins for Q9V0T9 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V0T9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutamyl-tRNA(Gln) amidotransferase subunit E
C, D
633Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 0 
Gene Names: gatE
EC: 6.3.5.-
Find proteins for Q9V0U0 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V0U0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ASP
Query on ASP

Download SDF File 
Download CCD File 
A, B
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 102.700α = 90.00
b = 138.200β = 109.60
c = 134.400γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
CNSrefinement
SHARPphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance