8JE5 | pdb_00008je5

Crystal Structure of Anopheles culicifacies Prolyl-tRNA Synthetase (AcPRS) in complex with Halofuginone

PDB DOI: https://doi.org/10.2210/pdb8JE5/pdb

Classification: LIGASE/INHIBITOR
Organism(s): Anopheles culicifacies
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-05-15 Released: 2024-11-27
Deposition Author(s): Goswami, R., Manickam, Y., Chhibber-Goel, J., Harlos, K., Sharma, A.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.280 (Depositor), 0.277 (DCC)
R-Value Work:
0.206 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Chemical targeting of prolyl-tRNA synthetase stalls ovarian development and kills malaria vectors.

Goswami, R., Manickam, Y., Goel, J.C., Gupta, S., B M, S., Sharma, A.

(2025) J Infect Dis

PubMed: 40048639 Search on PubMed
DOI: https://doi.org/10.1093/infdis/jiaf095
Primary Citation Related Structures:
8JE5, 8JE6, 8JE7

PubMed Abstract:
Along with rising resistance to antimalarials, the emergence of insecticide resistance in Anopheles mosquito species also remains a serious concern. Here, we reveal two potent compounds that show larvicidal and endectocidal activity against malaria vectors, Anopheles culicifacies and Anopheles stephensi, respectively. We investigated larvicidal activity of two inhibitors against III-instar larvae of Anopheles culicifacies. The survival and fertility of adult female Anopheles stephensi mosquitoes were assessed. Additionally, we purified recombinant prolyl-tRNA synthetase of Anopheles culicifacies and performed enzyme-based assays and structural analysis with the two inhibitors. Our study reveals that the Anopheles culicifacies prolyl-tRNA synthetase (AcProRS) is potently inhibited by halofuginone (HFG) and an ATP mimetic (L95). The evaluation of larvicidal activity of HFG against Anopheles culicifacies III-instar larvae showed a dose-dependent increase in mortality. In adult female Anopheles stephensi mosquitoes, ingestion of HFG via artificial blood feeding resulted in impaired ovary development, reduced egg laying, and decreased overall survival. The potent enzymatic inhibition of AcProRS thus drives the killing of larvae. The co-crystal structure of AcProRS with inhibitors provides a structural basis for improving their potency as future larvicides. Our data suggest the potential for repositioning halofuginone (HFG) and pyrrolidine-based ATP-mimetics (L95) as larvicides. Targeting the vector-encoded aminoacyl-tRNA synthetases provides a new focus for developing effective agents that can control multiple mosquitoe-borne infectious diseases like malaria and dengue.

Organizational Affiliation

ICMR-National Institute of Malaria Research (NIMR); Delhi, India.

Macromolecule Content

Total Structure Weight: 117.54 kDa
Atom Count: 7,590
Modeled Residue Count: 970
Deposited Residue Count: 1,010
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROLYL-TRNA SYNTHETASE	A, B	505	Anopheles culicifacies	Mutation(s): 0 EC: 6.1.1.17 (UniProt), 6.1.1.15 (UniProt)
UniProt
Find proteins for A0A182M1F8 (Anopheles culicifacies) Explore A0A182M1F8 Go to UniProtKB: A0A182M1F8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A182M1F8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HFG (Subject of Investigation/LOI) Query on HFG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one C₁₆ H₁₇ Br Cl N₃ O₃ LVASCWIMLIKXLA-CABCVRRESA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B]