4RRB

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/ncomms8552
  • Primary Citation of Related Structures:  
    4RR6, 4RR7, 4RR8, 4RR9, 4RRA, 4RRB, 4RRC, 4RRD, 4RRF, 4RRG, 4RRH, 4RRI, 4RRJ, 4RRK, 4RRL, 4RRM, 4RRQ, 4RRR

  • 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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable threonine--tRNA ligase 2136Aeropyrum pernix K1Mutation(s): 0 
Gene Names: thrS2APE_0117.1
EC: 6.1.1.3
UniProt
Find proteins for Q9YFY3 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YFY3 
Go to UniProtKB:  Q9YFY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YFY3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A3T
Query on A3T

Download Ideal Coordinates CCD File 
B [auth A]3'-deoxy-3'-(L-threonylamino)adenosine
C14 H21 N7 O5
JYCQZCJEBNTMCV-JHJLZTHQSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
A3T Binding MOAD:  4RRB Kd: 1.34e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.101α = 90
b = 47.101β = 90
c = 112.686γ = 90
Software Package:
Software NamePurpose
AUTOMARdata collection
MOLREPphasing
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations