8S65 | pdb_00008s65

1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) as target for anti Toxoplasma gondii compounds: crystal structure, biochemical characterization and biological evaluation of inhibitors

PDB DOI: https://doi.org/10.2210/pdb8S65/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Toxoplasma gondii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-26 Released: 2024-08-21
Deposition Author(s): Mazzone, F., Hoeppner, A., Reiners, J., Applegate, V., Abdullaziz, M., Gottstein, J., Wesemann, M., Kurz, T., Smits, S.H., Pfeffer, K.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.225 (Depositor), 0.227 (DCC)
R-Value Work:
0.194 (Depositor), 0.198 (DCC)
R-Value Observed:
0.196 (Depositor)

Method: SOLUTION SCATTERING

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

1-Deoxy-d-xylulose 5-phosphate reductoisomerase as target for anti Toxoplasma gondii agents: crystal structure, biochemical characterization and biological evaluation of inhibitors.

Mazzone, F., Hoeppner, A., Reiners, J., Gertzen, C.G.W., Applegate, V., Abdullaziz, M.A., Gottstein, J., Degrandi, D., Wesemann, M., Kurz, T., Smits, S.H.J., Pfeffer, K.

(2024) Biochem J 481: 1075-1096

PubMed: 39105673 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1042/BCJ20240110
Primary Citation Related Structures:
8S65

PubMed Abstract:
Toxoplasma gondii is a widely distributed apicomplexan parasite causing toxoplasmosis, a critical health issue for immunocompromised individuals and for congenitally infected foetuses. Current treatment options are limited in number and associated with severe side effects. Thus, novel anti-toxoplasma agents need to be identified and developed. 1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) is considered the rate-limiting enzyme in the non-mevalonate pathway for the biosynthesis of the isoprenoid precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate in the parasite, and has been previously investigated for its key role as a novel drug target in some species, encompassing Plasmodia, Mycobacteria and Escherichia coli. In this study, we present the first crystal structure of T. gondii DXR (TgDXR) in a tertiary complex with the inhibitor fosmidomycin and the cofactor NADPH in dimeric conformation at 2.5 Å resolution revealing the inhibitor binding mode. In addition, we biologically characterize reverse α-phenyl-β-thia and β-oxa fosmidomycin analogues and show that some derivatives are strong inhibitors of TgDXR which also, in contrast with fosmidomycin, inhibit the growth of T. gondii in vitro. Here, ((3,4-dichlorophenyl)((2-(hydroxy(methyl)amino)-2-oxoethyl)thio)methyl)phosphonic acid was identified as the most potent anti T. gondii compound. These findings will enable the future design and development of more potent anti-toxoplasma DXR inhibitors.

Organizational Affiliation

Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, Düsseldorf, Germany.

Macromolecule Content

Total Structure Weight: 105.8 kDa
Atom Count: 6,416
Modeled Residue Count: 821
Deposited Residue Count: 944
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose-5-phosphate reductoisomerase	A, B	472	Toxoplasma gondii	Mutation(s): 0 Gene Names: TGME49_214850 EC: 1.1.1.267
UniProt
Find proteins for S8ESX0 (Toxoplasma gondii (strain ATCC 50611 / Me49)) Explore S8ESX0 Go to UniProtKB: S8ESX0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S8ESX0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
FOM Query on FOM Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID C₄ H₁₀ N O₅ P GJXWDTUCERCKIX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	F [auth A], G [auth A], H [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]