4NU7

2.05 Angstrom Crystal Structure of Ribulose-phosphate 3-epimerase from Toxoplasma gondii.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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
Ribulose-phosphate 3-epimeraseA, B, C, D246Toxoplasma gondiiMutation(s): 0 
Gene Names: RPETGVEG_004130
EC: 5.1.3.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
Q [auth B],
R [auth B],
U [auth C],
V [auth C],
X [auth D],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
O [auth B],
T [auth C],
W [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
M [auth B],
N [auth B],
S [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.51α = 90
b = 138.51β = 90
c = 349.329γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2021-01-27
    Changes: Database references, Derived calculations