3PD2

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: 1.86 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanistic insights into cognate substrate discrimination during proofreading in translation

Hussain, T.Kamarthapu, V.Kruparani, S.P.Deshmukh, M.V.Sankaranarayanan, R.

(2010) Proc.Natl.Acad.Sci.USA 107: 22117-22121

  • DOI: 10.1073/pnas.1014299107
  • Primary Citation of Related Structures:  3PD3, 3PD4, 3PD5

  • PubMed Abstract: 
  • Editing/proofreading by aminoacyl-tRNA synthetases is an important quality control step in the accurate translation of the genetic code that removes noncognate amino acids attached to tRNA. Defects in the process of editing result in disease conditio ...

    Editing/proofreading by aminoacyl-tRNA synthetases is an important quality control step in the accurate translation of the genetic code that removes noncognate amino acids attached to tRNA. Defects in the process of editing result in disease conditions including neurodegeneration. While proofreading, the cognate amino acids larger by a methyl group are generally thought to be sterically rejected by the editing modules as envisaged by the "Double-Sieve Model." Strikingly using solution based direct binding studies, NMR-heteronuclear single quantum coherence (HSQC) and isothermal titration calorimetry experiments, with an editing domain of threonyl-tRNA synthetase, we show that the cognate substrate can gain access and bind to the editing pocket. High-resolution crystal structural analyses reveal that functional positioning of substrates rather than steric exclusion is the key for the mechanism of discrimination. A strategically positioned "catalytic water" molecule is excluded to avoid hydrolysis of the cognate substrate using a "RNA mediated substrate-assisted catalysis mechanism" at the editing site. The mechanistic proof of the critical role of RNA in proofreading activity is a completely unique solution to the problem of cognate-noncognate selection mechanism.


    Organizational Affiliation

    Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007, 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A3SKd: 3400 nM BINDINGMOAD
A3SKd: 3400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.227α = 90.00
b = 66.334β = 90.00
c = 93.177γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-03-05
    Type: Database references