2HL1

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with seryl-3'-aminoadenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea

Hussain, T.Kruparani, S.P.Pal, B.Dock-Bregeon, A.C.Dwivedi, S.Shekar, M.R.Sureshbabu, K.Sankaranarayanan, R.

(2006) Embo J. 25: 4152-4162

  • DOI: 10.1038/sj.emboj.7601278
  • Primary Citation of Related Structures:  2HKZ, 2HL0, 2HL2

  • PubMed Abstract: 
  • To ensure a high fidelity during translation, threonyl-tRNA synthetases (ThrRSs) harbor an editing domain that removes noncognate L-serine attached to tRNAThr. Most archaeal ThrRSs possess a unique editing domain structurally similar to D-aminoacyl-t ...

    To ensure a high fidelity during translation, threonyl-tRNA synthetases (ThrRSs) harbor an editing domain that removes noncognate L-serine attached to tRNAThr. Most archaeal ThrRSs possess a unique editing domain structurally similar to D-aminoacyl-tRNA deacylases (DTDs) found in eubacteria and eukaryotes that specifically removes D-amino acids attached to tRNA. Here, we provide mechanistic insights into the removal of noncognate L-serine from tRNAThr by a DTD-like editing module from Pyrococcus abyssi ThrRS (Pab-NTD). High-resolution crystal structures of Pab-NTD with pre- and post-transfer substrate analogs and with L-serine show mutually nonoverlapping binding sites for the seryl moiety. Although the pre-transfer editing is excluded, the analysis reveals the importance of main chain atoms in proper positioning of the post-transfer substrate for its hydrolysis. A single residue has been shown to play a pivotal role in the inversion of enantioselectivity both in Pab-NTD and DTD. The study identifies an enantioselectivity checkpoint that filters opposite chiral molecules and thus provides a fascinating example of how nature has subtly engineered this domain for the selection of chiral molecules during translation.


    Related Citations: 
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Threonyl-tRNA synthetase
A, B
147Pyrococcus abyssi (strain GE5 / Orsay)Gene Names: thrS
EC: 6.1.1.3
Find proteins for Q9UZ14 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9UZ14
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A3S
Query on A3S

Download SDF File 
Download CCD File 
A, B
SERINE-3'-AMINOADENOSINE
N'-L-SERYL-3'-AMINO-(3'-DEOXY)-ADENOSINE
C13 H19 N7 O5
ITDKSTILAWHDJI-AYEBZEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.991α = 90.00
b = 75.735β = 90.00
c = 95.294γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CCP4phasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance