7ROU

Structure of human tyrosyl tRNA synthetase in complex with ML901-Tyr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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, cytoplasmic365Homo sapiensMutation(s): 0 
Gene Names: YARS1YARS
EC: 6.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54577 (Homo sapiens)
Explore P54577 
Go to UniProtKB:  P54577
PHAROS:  P54577
GTEx:  ENSG00000134684 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54577
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
66I (Subject of Investigation/LOI)
Query on 66I

Download Ideal Coordinates CCD File 
B [auth A]{(2R,3S,4R,5R)-5-[4-amino-3-(difluoromethoxy)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-dihydroxyoxolan-2-yl}methyl [(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]sulfamate (non-preferred name)
C20 H23 F2 N7 O9 S
MUBAQGITUFCKMG-IFHUHSRSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.622α = 90
b = 162.189β = 90
c = 35.231γ = 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