4QFH | pdb_00004qfh

Structure of a glucose-6-phosphate isomerase from Trypanosoma cruzi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.174 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.139 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.141 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural Characterization of Glycolytic Enzymes from Trypanosoma cruzi.

Austin, K.Obachi, V.A.Muzenda, F.L.Moetlediwa, M.T.Agyei, C.Craig, T.Abendroth, J.Edwards, T.Nguyen, M.Tran, N.Staker, B.Subramanian, S.Myler, P.Zininga, T.Govender, K.K.Chakafana, G.

(2026) Mol Biochem Parasitol : 111736-111736

  • DOI: https://doi.org/10.1016/j.molbiopara.2026.111736
  • Primary Citation of Related Structures:  
    4G7F, 4QFH

  • PubMed Abstract: 

    Trypanosoma cruzi, the etiological agent of Chagas disease, depends on glycolysis for ATP production, rendering its glycolytic enzymes attractive targets for therapeutic development. Here, we report the high-resolution crystal structures of two essential glycolytic enzymes, glucose-6-phosphate isomerase (Tc PGI, 1.8 Å) and enolase (Tc enolase, 2.4 Å) and provide structural and computational analyses to support structure-based drug design. Tc PGI adopts a dimeric αβα sandwich fold and features a parasite-specific 53-residue N-terminal extension and a unique C-terminal hook region which both distinguish it from its human ortholog. Tc enolase exhibits the conserved (α/β) 8 TIM barrel fold but harbors minor distinct structural deviations, including an extended α17 helix and a structured α1 region, which differentiate it from human isoforms. Both enzymes exhibited high thermal stability, consistent with adaptation to the parasite's complex life cycle. Structure-based virtual screening using a scaffold with known multi-target potential identified distinct high-affinity inhibitors for each enzyme. Molecular dynamics simulations further confirmed stable enzyme-inhibitor interactions and favorable binding energetics. Collectively, these findings reveal structural signatures unique to T. cruzi glycolytic enzymes and lay the groundwork for the development of antiparasitic therapeutics.


  • Organizational Affiliation
    • Chemistry and Biochemistry Department, Hampton University, 200 William R Harvey Way, Hampton, VA 23668, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-6-phosphate isomerase
A, B
616Trypanosoma cruziMutation(s): 0 
Gene Names: Tc00.1047053506529.508TcC31.19
EC: 5.3.1.9
UniProt
Find proteins for Q4E5N1 (Trypanosoma cruzi (strain CL Brener))
Explore Q4E5N1 
Go to UniProtKB:  Q4E5N1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4E5N1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.174 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.139 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.141 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.84α = 90
b = 127.03β = 109.74
c = 72.4γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2026-03-04
    Changes: Database references, Structure summary