7BY6 | pdb_00007by6

Plasmodium vivax cytoplasmic Phenylalanyl-tRNA synthetase in complex with BRD1389

• PDB DOI: https://doi.org/10.2210/pdb7BY6/pdb

• Classification: LIGASE
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-21 Released: 2020-11-04 
• Deposition Author(s): Malhotra, N., Manmohan, S., Harlos, K., Melillo, B., Schreiber, S.L., Manickam, Y., Sharma, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.288 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Structural basis of malaria parasite phenylalanine tRNA-synthetase inhibition by bicyclic azetidines.

Sharma, M., Malhotra, N., Yogavel, M., Harlos, K., Melillo, B., Comer, E., Gonse, A., Parvez, S., Mitasev, B., Fang, F.G., Schreiber, S.L., Sharma, A.

(2021) Nat Commun 12: 343-343

• PubMed: 33436639 
• DOI: https://doi.org/10.1038/s41467-020-20478-5
• Primary Citation Related Structures: 
  7BY6


• PubMed Abstract: 
  

  The inhibition of Plasmodium cytosolic phenylalanine tRNA-synthetase (cFRS) by a novel series of bicyclic azetidines has shown the potential to prevent malaria transmission, provide prophylaxis, and offer single-dose cure in animal models of malaria. To date, however, the molecular basis of Plasmodium cFRS inhibition by bicyclic azetidines has remained unknown. Here, we present structural and biochemical evidence that bicyclic azetidines are competitive inhibitors of L-Phe, one of three substrates required for the cFRS-catalyzed aminoacylation reaction that underpins protein synthesis in the parasite. Critically, our co-crystal structure of a PvcFRS-BRD1389 complex shows that the bicyclic azetidine ligand binds to two distinct sub-sites within the PvcFRS catalytic site. The ligand occupies the L-Phe site along with an auxiliary cavity and traverses past the ATP binding site. Given that BRD1389 recognition residues are conserved amongst apicomplexan FRSs, this work lays a structural framework for the development of drugs against both Plasmodium and related apicomplexans.

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Organizational Affiliation: 
• Molecular Medicine, Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India.
Division of Structural Biology, Welcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, England.
Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA.
Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
Eisai Inc., 35 Cambridgepark Drive Suite 200, Cambridge, MA, 02140, USA.
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.
Molecular Medicine, Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India. [e-mail].
National Institute of Malarial Research, Sector 8 Dwarka, New Delhi, 110077, India. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 107.45 kDa 
• Atom Count: 6,924 
• Modeled Residue Count: 905 
• Deposited Residue Count: 917 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanyl-tRNA synthetase beta chain, putative	A	299	Plasmodium vivax	Mutation(s): 0  Gene Names: PVX_081300 EC: 6.1.1.20
UniProt
Find proteins for A5K9S0 (Plasmodium vivax (strain Salvador I)) Explore A5K9S0  Go to UniProtKB:  A5K9S0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanyl-tRNA synthetase beta chain, putative	B	618	Plasmodium vivax	Mutation(s): 0  Gene Names: PVX_090880 EC: 6.1.1.20
UniProt
Find proteins for A5K464 (Plasmodium vivax (strain Salvador I)) Explore A5K464  Go to UniProtKB:  A5K464

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FB9 (Subject of Investigation/LOI)	C [auth A]	(3S,4R,8R,9R,10S)-N-(4-cyclopropyloxyphenyl)-10-(methoxymethyl)-3,4-bis(oxidanyl)-9-[4-(2-phenylethynyl)phenyl]-1,6-diazabicyclo[6.2.0]decane-6-carboxamide C34 H37 N3 O5 DJCBDEOPQMQGCA-AXJMTRDLSA-N
MG (Subject of Investigation/LOI)	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.288 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.523	α = 90
b = 74.071	β = 90
c = 121.682	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-04 
Deposition Author(s): Malhotra, N., Manmohan, S., Harlos, K., Melillo, B., Schreiber, S.L., Manickam, Y., Sharma, S.

Revision History  

• Version 1.0: 2020-11-04
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description