7ROU | pdb_00007rou

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

• PDB DOI: https://doi.org/10.2210/pdb7ROU/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-08-02 Released: 2022-06-08 
• Deposition Author(s): Metcalfe, R.D., Xie, S.C., Morton, C.J., Tilley, L., Griffin, M.D.W.
• Funding Organization(s): Global Health Innovative Technology Fund, National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

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

• PubMed: 35653481 
• DOI: https://doi.org/10.1126/science.abn0611
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia.
Takeda Development Center Americas, Inc., Cambridge, MA 02139, USA.
Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.
University of Basel, 4003 Basel, Switzerland.
Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia.
Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
Drug Delivery, Disposition, and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia.
Medicines for Malaria Venture, P.O. Box 1826, 20, Route de Pré-Bois, 1215 Geneva 15, Switzerland.
Seofon Consulting, Natick, MA 01760, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 42.37 kDa 
• Atom Count: 3,060 
• Modeled Residue Count: 335 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine--tRNA ligase, cytoplasmic	A	365	Homo sapiens	Mutation(s): 0  Gene Names: YARS1, YARS 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
66I (Subject of Investigation/LOI)	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	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 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.622	α = 90
b = 162.189	β = 90
c = 35.231	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Metcalfe, R.D., Xie, S.C., Morton, C.J., Tilley, L., Griffin, M.D.W.

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Funding Organization	Location	Grant Number
Global Health Innovative Technology Fund	Japan	GHIT-RFP-HTLP-H2019-104
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1171794

Revision History  

• 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