Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.48 kDa 
• Atom Count: 2915 
• Modelled Residue Count: 314 
• Deposited Residue Count: 328 
• Unique protein chains: 1

4NBI

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

• PDB DOI: 10.2210/pdb4NBI/pdb

• Classification: HYDROLASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-23 Released: 2013-12-18 
• Deposition Author(s): Ahmad, S., Routh, S.B., Kamarthapu, V., Sankaranarayanan, R.

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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 

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

• PubMed: 24302572 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-tyrosyl-tRNA(Tyr) deacylase	A, B	164	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: dtd, PF11_0095, PF3D7_1108200 EC: 3.1 (PDB Primary Data), 3.1.1.96 (UniProt)
UniProt
Find proteins for Q8IIS0 (Plasmodium falciparum (isolate 3D7)) Explore Q8IIS0  Go to UniProtKB:  Q8IIS0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D3Y	C [auth A], E [auth B]	3'-deoxy-3'-(D-tyrosylamino)adenosine C19 H23 N7 O5 GCCJIIJWAJOTAC-XDJZACDYSA-N
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

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 = 82.134	α = 90
b = 65.743	β = 93.3
c = 56.917	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-23 
• Released Date: 2013-12-18 
Deposition Author(s): Ahmad, S., Routh, S.B., Kamarthapu, V., Sankaranarayanan, R.

Revision History  

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