7ROR

Plasmodium falciparum tyrosyl-tRNA synthetase in complex with tyrosine-AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Reaction hijacking of tyrosine tRNA synthetase as a new whole-of-life-cycle antimalarial strategy.

Xie, S.C.Metcalfe, R.D.Dunn, E.Morton, C.J.Huang, S.C.Puhalovich, T.Du, Y.Wittlin, S.Nie, S.Luth, M.R.Ma, L.Kim, M.S.Pasaje, C.F.A.Kumpornsin, K.Giannangelo, C.Houghton, F.J.Churchyard, A.Famodimu, M.T.Barry, D.C.Gillett, D.L.Dey, S.Kosasih, C.C.Newman, W.Niles, J.C.Lee, M.C.S.Baum, J.Ottilie, S.Winzeler, E.A.Creek, D.J.Williamson, N.Parker, M.W.Brand, S.Langston, S.P.Dick, L.R.Griffin, M.D.W.Gould, A.E.Tilley, L.

(2022) Science 376: 1074-1079

  • DOI: https://doi.org/10.1126/science.abn0611
  • Primary Citation of Related Structures:  
    7ROR, 7ROS, 7ROT, 7ROU

  • PubMed Abstract: 

    Aminoacyl transfer RNA (tRNA) synthetases (aaRSs) are attractive drug targets, and we present class I and II aaRSs as previously unrecognized targets for adenosine 5'-monophosphate-mimicking nucleoside sulfamates. The target enzyme catalyzes the formation of an inhibitory amino acid-sulfamate conjugate through a reaction-hijacking mechanism. We identified adenosine 5'-sulfamate as a broad-specificity compound that hijacks a range of aaRSs and ML901 as a specific reagent a specific reagent that hijacks a single aaRS in the malaria parasite Plasmodium falciparum , namely tyrosine RS ( Pf YRS). ML901 exerts whole-life-cycle-killing activity with low nanomolar potency and single-dose efficacy in a mouse model of malaria. X-ray crystallographic studies of plasmodium and human YRSs reveal differential flexibility of a loop over the catalytic site that underpins differential susceptibility to reaction hijacking by ML901.


  • Organizational Affiliation

    Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine--tRNA ligase
A, B
374Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0807900
EC: 6.1.1.1
UniProt
Find proteins for Q8IAR7 (Plasmodium falciparum (isolate 3D7))
Explore Q8IAR7 
Go to UniProtKB:  Q8IAR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IAR7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
69X (Subject of Investigation/LOI)
Query on 69X

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
5'-O-[(S)-{[(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]oxy}(hydroxy)phosphoryl]adenosine
C19 H23 N6 O9 P
NFCVQVDMLQEZAK-URQYDQELSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B],
K [auth B]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.612α = 90
b = 46.597β = 93.806
c = 141.402γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Global Health Innovative Technology FundJapanGHIT-RFP-HTLP-H2019-104
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1171794

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description