4RRQ

K121M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi with L-Ser3AA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.

Ahmad, S.Muthukumar, S.Kuncha, S.K.Routh, S.B.Yerabham, A.S.Hussain, T.Kamarthapu, V.Kruparani, S.P.Sankaranarayanan, R.

(2015) Nat Commun 6: 7552-7552

  • DOI: 10.1038/ncomms8552
  • Primary Citation of Related Structures:  
    4RRL, 4RRM, 4RRQ, 4RRR, 4RRD, 4RRF, 4RRG, 4RRH, 4RRI, 4RRJ

  • PubMed Abstract: 
  • Proofreading modules of aminoacyl-tRNA synthetases are responsible for enforcing a high fidelity during translation of the genetic code. They use strategically positioned side chains for specifically targeting incorrect aminoacyl-tRNAs. Here, we show that a unique proofreading module possessing a D-aminoacyl-tRNA deacylase fold does not use side chains for imparting specificity or for catalysis, the two hallmark activities of enzymes ...

    Proofreading modules of aminoacyl-tRNA synthetases are responsible for enforcing a high fidelity during translation of the genetic code. They use strategically positioned side chains for specifically targeting incorrect aminoacyl-tRNAs. Here, we show that a unique proofreading module possessing a D-aminoacyl-tRNA deacylase fold does not use side chains for imparting specificity or for catalysis, the two hallmark activities of enzymes. We show, using three distinct archaea, that a side-chain-stripped recognition site is fully capable of solving a subtle discrimination problem. While biochemical probing establishes that RNA plays the catalytic role, mechanistic insights from multiple high-resolution snapshots reveal that differential remodelling of the catalytic core at the RNA-peptide interface provides the determinants for correct proofreading activity. The functional crosstalk between RNA and protein elucidated here suggests how primordial enzyme functions could have emerged on RNA-peptide scaffolds before recruitment of specific side chains.


    Organizational Affiliation

    Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Threonine--tRNA ligaseA, B147Pyrococcus abyssi GE5Mutation(s): 1 
Gene Names: thrSPYRAB13430PAB1490
EC: 6.1.1.3
Find proteins for Q9UZ14 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9UZ14 
Go to UniProtKB:  Q9UZ14
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A3S
Query on A3S

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]SERINE-3'-AMINOADENOSINE
C13 H19 N7 O5
ITDKSTILAWHDJI-AYEBZEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.584α = 90
b = 74.589β = 90
c = 96.309γ = 90
Software Package:
Software NamePurpose
AUTOMARdata collection
MOLREPphasing
PHASERphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description