4O0N

2.4 Angstrom Resolution Crystal Structure of Putative Nucleoside Diphosphate Kinase from Toxoplasma gondii.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii .

Lykins, J.D.Filippova, E.V.Halavaty, A.S.Minasov, G.Zhou, Y.Dubrovska, I.Flores, K.J.Shuvalova, L.A.Ruan, J.El Bissati, K.Dovgin, S.Roberts, C.W.Woods, S.Moulton, J.D.Moulton, H.McPhillie, M.J.Muench, S.P.Fishwick, C.W.G.Sabini, E.Shanmugam, D.Roos, D.S.McLeod, R.Anderson, W.F.Ngo, H.M.

(2018) Front Cell Infect Microbiol 8: 352-352

  • DOI: https://doi.org/10.3389/fcimb.2018.00352
  • Primary Citation of Related Structures:  
    4NML, 4NOG, 4NU7, 4O0N, 4ODI, 5BXI

  • PubMed Abstract: 

    Toxoplasma gondii , an Apicomplexan parasite, causes significant morbidity and mortality, including severe disease in immunocompromised hosts and devastating congenital disease, with no effective treatment for the bradyzoite stage. To address this, we used the Tropical Disease Research database, crystallography, molecular modeling, and antisense to identify and characterize a range of potential therapeutic targets for toxoplasmosis. Phosphoglycerate mutase II (PGMII), nucleoside diphosphate kinase (NDK), ribulose phosphate 3-epimerase (RPE), ribose-5-phosphate isomerase (RPI), and ornithine aminotransferase (OAT) were structurally characterized. Crystallography revealed insights into the overall structure, protein oligomeric states and molecular details of active sites important for ligand recognition. Literature and molecular modeling suggested potential inhibitors and druggability. The targets were further studied with vivoPMO to interrupt enzyme synthesis, identifying the targets as potentially important to parasitic replication and, therefore, of therapeutic interest. Targeted vivoPMO resulted in statistically significant perturbation of parasite replication without concomitant host cell toxicity, consistent with a previous CRISPR/Cas9 screen showing PGM, RPE, and RPI contribute to parasite fitness. PGM, RPE, and RPI have the greatest promise for affecting replication in tachyzoites. These targets are shared between other medically important parasites and may have wider therapeutic potential.


  • Organizational Affiliation

    Pritzker School of Medicine, University of Chicago, Chicago, IL, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
171Toxoplasma gondii ME49Mutation(s): 0 
Gene Names: TGME49_295350
EC: 2.7.4.6
UniProt
Find proteins for B9Q287 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9Q287 
Go to UniProtKB:  B9Q287
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9Q287
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth B]
P [auth C]
Q [auth D]
M [auth A],
N [auth B],
O [auth B],
P [auth C],
Q [auth D],
R [auth E],
S [auth E],
T [auth F],
U [auth G],
V [auth H],
W [auth I],
X [auth J],
Y [auth K],
Z [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.385α = 90
b = 121.591β = 90
c = 212.274γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references, Structure summary
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2021-01-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Refinement description