4RRD

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA (snapshot 4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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, 4RRK, 4RRA, 4RRB, 4RRC, 4RR6, 4RR7, 4RR8, 4RR9

  • 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
Probable threonine--tRNA ligase 2A136Aeropyrum 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A3T (Subject of Investigation/LOI)
Query on A3T

Download Ideal Coordinates CCD File 
B [auth A]3'-deoxy-3'-(L-threonylamino)adenosine
C14 H21 N7 O5
JYCQZCJEBNTMCV-JHJLZTHQSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
A3T Binding MOAD:  4RRD Kd: 1.34e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.532α = 90
b = 47.532β = 90
c = 113.556γ = 90
Software Package:
Software NamePurpose
CrystalCleardata 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