2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 from Toxoplasma gondii

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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

    Illinois Math and Science Academy, Aurora, IL, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerate mutase PGMII
A, B, C, D
281Toxoplasma gondii ME49Mutation(s): 0 
Gene Names: PGMIITGME49_297060
EC: (PDB Primary Data), (UniProt)
Find proteins for S8GJT7 (Toxoplasma gondii (strain ATCC 50611 / Me49))
Explore S8GJT7 
Go to UniProtKB:  S8GJT7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS8GJT7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.182α = 90
b = 149.474β = 90
c = 72.12γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

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