7WAO | pdb_00007wao

Glutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) in complex with Mn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 
    0.246 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural characterization of glutamyl-tRNA synthetase (GluRS) from Plasmodium falciparum.

Sharma, V.K.Chhibber-Goel, J.Yogavel, M.Sharma, A.

(2022) Mol Biochem Parasitol 253: 111530-111530

  • DOI: https://doi.org/10.1016/j.molbiopara.2022.111530
  • Primary Citation Related Structures: 
    7WAI, 7WAJ, 7WAK, 7WAL, 7WAO

  • PubMed Abstract: 

    Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes in protein translation machinery that provide the charged tRNAs needed for protein synthesis. Over the past decades, aaRSs have been studied as anti-parasitic, anti-bacterial, and anti-fungal drug targets. This study focused on the cytoplasmic glutamyl-tRNA synthetase (GluRS) from Plasmodium falciparum, which belongs to class Ib in aaRSs. GluRS unlike most other aaRSs requires tRNA to activate its cognate amino acid substrate L-Glutamate (L-Glu), and fails to form an intermediate adenylate complex in the absence of tRNA. The crystal structures of the Apo, ATP, and ADP-bound forms of Plasmodium falciparum glutamyl-tRNA synthetase (PfGluRS) were solved at 2.1 Å, 2.2 Å, and 2.8 Å respectively. The structural comparison of the Apo- and ATP-bound holo-forms of PfGluRS showed considerable conformational changes in the loop regions around the ATP-binding pocket of the enzyme. Biophysical characterization of the PfGluRS showed binding of the enzyme substrates L-Gluand ATP.. The sequence and structural conservation were evident across GluRS compared to other species. The structural dissection of the PfGluRS gives insight into the critical residues involved in the binding of ATP substrate, which can be harvested to develop new antimalarial drugs.


  • Organizational Affiliation
    • Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India.

Macromolecule Content 

  • Total Structure Weight: 61.76 kDa 
  • Atom Count: 3,962 
  • Modeled Residue Count: 502 
  • Deposited Residue Count: 523 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamyl-tRNA synthetase523Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1349200
EC: 6.1.1.17
UniProt
Find proteins for Q8IDK7 (Plasmodium falciparum (isolate 3D7))
Explore Q8IDK7 
Go to UniProtKB:  Q8IDK7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IDK7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
(Subject of Investigation/LOI)

Query on MN



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
(Subject of Investigation/LOI)

Query on CL



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free:  0.246 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.75α = 90
b = 46.88β = 108.88
c = 94.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaPR32713

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary