1ZQ1

Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.str.2005.06.016
  • Primary Citation of Related Structures:  
    1ZQ1

  • 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(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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit D
A, B
438Pyrococcus abyssiMutation(s): 15 
Gene Names: gatD
EC: 6.3.5
UniProt
Find proteins for Q9V0T9 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V0T9 
Go to UniProtKB:  Q9V0T9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V0T9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit E
C, D
633Pyrococcus abyssiMutation(s): 0 
Gene Names: gatE
EC: 6.3.5
UniProt
Find proteins for Q9V0U0 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V0U0 
Go to UniProtKB:  Q9V0U0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V0U0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.7α = 90
b = 138.2β = 109.6
c = 134.4γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
SHARPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary