1Y2Q

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi

• PDB DOI: https://doi.org/10.2210/pdb1Y2Q/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus abyssi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-11-23 Released: 2005-06-14 
• Deposition Author(s): Dwivedi, S., Kruparani, S.P., Sankaranarayanan, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.272 
• R-Value Work: 0.205 
• R-Value Observed: 0.209 

Literature

A D-amino acid editing module coupled to the translational apparatus in archaea

Dwivedi, S., Kruparani, S.P., Sankaranarayanan, R.

(2005) Nat Struct Mol Biol 12: 556-557

• PubMed: 15908961 
• DOI: https://doi.org/10.1038/nsmb943
• Primary Citation of Related Structures:  
  1Y2Q


• PubMed Abstract: 
  

  We report the crystal structure of an archaea-specific editing domain of threonyl-tRNA synthetase that reveals a marked structural similarity to D-amino acid deacylases found in eubacteria and eukaryotes. The domain can bind D-amino acids despite a low sequence identity to other D-amino acid deacylases. These results together indicate the presence of these deacylases in all three kingdoms of life. This underlines an important role they may have played in enforcing homochirality during translation.

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Organizational Affiliation: 

Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.28 kDa 
• Atom Count: 1,316 
• Modelled Residue Count: 143 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonyl-tRNA synthetase	A	143	Pyrococcus abyssi	Mutation(s): 0  Gene Names: thrS EC: 6.1.1.3
UniProt
Find proteins for Q9UZ14 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9UZ14  Go to UniProtKB:  Q9UZ14

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.272 
• R-Value Work: 0.205 
• R-Value Observed: 0.209 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.752	α = 90
b = 61.752	β = 90
c = 64.894	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-14 
Deposition Author(s): Dwivedi, S., Kruparani, S.P., Sankaranarayanan, R.

Revision History  

• Version 1.0: 2005-06-14
  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: 2024-03-13
  Changes: Data collection, Database references