3VGJ

Crystal of Plasmodium falciparum tyrosyl-tRNA synthetase (PfTyrRS)in complex with adenylate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.212 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Malaria parasite tyrosyl-tRNA synthetase secretion triggers pro-inflammatory responses.

Bhatt, T.K.Khan, S.Dwivedi, V.P.Banday, M.M.Sharma, A.Chandele, A.Camacho, N.de Pouplana, L.R.Wu, Y.Craig, A.G.Mikkonen, A.T.Maier, A.G.Yogavel, M.Sharma, A.

(2011) Nat Commun 2: 530-530

  • DOI: 10.1038/ncomms1522

  • PubMed Abstract: 
  • Malaria infection triggers pro-inflammatory responses in humans that are detrimental to host health. Parasite-induced enhancement in cytokine levels correlate with malaria-associated pathologies. Here we show that parasite tyrosyl-tRNA synthetase (Pf ...

    Malaria infection triggers pro-inflammatory responses in humans that are detrimental to host health. Parasite-induced enhancement in cytokine levels correlate with malaria-associated pathologies. Here we show that parasite tyrosyl-tRNA synthetase (PfTyrRS), a housekeeping protein translation enzyme, induces pro-inflammatory responses from host immune cells. PfTyrRS exits from the parasite cytoplasm into the infected red blood cell (iRBC) cytoplasm, from where it is released into the extracellular medium on iRBC lysis. Using its ELR peptide motif, PfTyrRS specifically binds to and internalizes into host macrophages, leading to enhanced secretion of the pro-inflammatory cytokines TNF-α and IL-6. PfTyrRS-macrophage interaction also augments expression of adherence-linked host endothelial receptors ICAM-1 and VCAM-1. Our description of PfTyrRS as a parasite-secreted protein that triggers pro-inflammatory host responses, along with its atomic resolution crystal structure in complex with tyrosyl-adenylate, provides a novel platform for targeting PfTyrRS in anti-parasitic strategies.


    Organizational Affiliation

    Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110 067, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-tRNA synthetase, putative
A, B
373Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 6.1.1.1
Find proteins for Q8IAR7 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IAR7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYR
Query on TYR

Download SDF File 
Download CCD File 
A, B
TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.212 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 137.560α = 90.00
b = 46.500β = 93.75
c = 141.350γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXrefinement
REFMACrefinement
MOLREPphasing
HKL-2000data scaling
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2015-03-04
    Type: Non-polymer description
  • Version 1.2: 2017-11-22
    Type: Refinement description