5BXI

1.7 Angstrom Resolution Crystal Structure of Putative Nucleoside Diphosphate Kinase from Toxoplasma gondii with Tyrosine of Tag Bound to Active Site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 ...

    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: 

    BrainMicro LLC, New Haven, CT, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
160Toxoplasma 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
Q [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
BCT
Query on BCT
Download Ideal Coordinates CCD File 
M [auth A],
N [auth B],
O [auth C],
P [auth D],
R [auth F],
M [auth A],
N [auth B],
O [auth C],
P [auth D],
R [auth F],
S [auth I]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 236.814α = 90
b = 73.4β = 116.83
c = 122.671γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
BLU-MAXdata collection
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary