4NBI

D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 1.86 Angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Mechanism of chiral proofreading during translation of the genetic code.

Ahmad, S., Routh, S.B., Kamarthapu, V., Chalissery, J., Muthukumar, S., Hussain, T., Kruparani, S.P., Deshmukh, M.V., Sankaranarayanan, R.

(2013) Elife 2: e01519-e01519

  • DOI: 10.7554/eLife.01519
  • Primary Citation of Related Structures:  
    4NBI, 4NBJ

  • PubMed Abstract: 

    • The biological macromolecular world is homochiral and effective enforcement and perpetuation of this homochirality is essential for cell survival. In this study, we present the mechanistic basis of a configuration-specific enzyme that selectively removes D-amino acids erroneously coupled to tRNAs ...

    The biological macromolecular world is homochiral and effective enforcement and perpetuation of this homochirality is essential for cell survival. In this study, we present the mechanistic basis of a configuration-specific enzyme that selectively removes D-amino acids erroneously coupled to tRNAs. The crystal structure of dimeric D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with a substrate-mimicking analog shows how it uses an invariant 'cross-subunit' Gly-cisPro dipeptide to capture the chiral centre of incoming D-aminoacyl-tRNA. While no protein residues are directly involved in catalysis, the unique side chain-independent mode of substrate recognition provides a clear explanation for DTD's ability to act on multiple D-amino acids. The strict chiral specificity elegantly explains how the enriched cellular pool of L-aminoacyl-tRNAs escapes this proofreading step. The study thus provides insights into a fundamental enantioselection process and elucidates a chiral enforcement mechanism with a crucial role in preventing D-amino acid infiltration during the evolution of translational apparatus. DOI: http://dx.doi.org/10.7554/eLife.01519.001.

    Organizational Affiliation: 

    Structural Biology Laboratory, Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Hyderabad, India.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-tyrosyl-tRNA(Tyr) deacylase A, B164Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: dtd, PF11_0095, PF3D7_1108200
EC: 3.1 (PDB Primary Data), 3.1.1.96 (UniProt)
Find proteins for Q8IIS0 (Plasmodium falciparum (isolate 3D7))
Explore Q8IIS0 
Go to UniProtKB:  Q8IIS0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D3Y
Query on D3Y
Download Ideal Coordinates CCD File 
A, B
3'-deoxy-3'-(D-tyrosylamino)adenosine
C19 H23 N7 O5
GCCJIIJWAJOTAC-XDJZACDYSA-N		 Ligand Interaction
PGE
Query on PGE
Download Ideal Coordinates CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.134α = 90
b = 65.743β = 93.3
c = 56.917γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Advisory, Refinement description