8GIL | pdb_00008gil

L-threonine 3-Dehydrogenase from Trypanosoma cruzi (apo form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Inhibition of L-threonine dehydrogenase from Trypanosoma cruzi reduces glycine and acetate production and interferes with parasite growth and viability.

Faria, J.D.N.Eufrasio, A.G.Fagundes, M.Lobo-Rojas, A.Marchese, L.de Lima Silva, C.C.Bezerra, E.H.S.Mercaldi, G.F.Alborghetti, M.R.Sforca, M.L.Cordeiro, A.T.

(2025) J Biological Chem 301: 108080-108080

  • DOI: https://doi.org/10.1016/j.jbc.2024.108080
  • Primary Citation of Related Structures:  
    8GIL, 8GJB

  • PubMed Abstract: 

    Trypanosoma cruzi is a flagellated protozoan and the etiological agent of Chagas disease, a neglected tropical disease described by Carlos Chagas in 1909 that remains without appropriate diagnostics and treatment. Throughout its life cycle, T. cruzi undergoes through many different environments, requiring adaptation of its metabolism to different nutrition sources. Recent studies have confirmed the adaptability of T. cruzi metabolism to different carbon sources and encouraged a deeper investigation of related metabolic pathways. In the present study, we investigated the catabolism of threonine in T. cruzi epimastigotes cultivated in LIT medium and following 24h of starvation in PBS. In LIT medium, threonine, serine, and histidine were rapidly consumed concomitantly with carbohydrates during parasite exponential growth. When threonine was provided as the only carbon source to starved parasites, they excreted acetate and glycine, corroborating the activity of a mitochondrial threonine degradation pathway. Subsequently, we used a recombinant T. cruzi L-threonine dehydrogrenase (TcTDH) to screen the Chagas Box, an open-source collection of phenotypic hits, and identified compound TCMDC-143160 as a low micromolar TcTDH inhibitor (IC50 = 3.5 μM). When TCMDC-143160 was administrated to starved parasites, it inhibited the threonine degradation pathway. Finally, we report the crystal structure of TcTDH and characterize its allosteric activation by potassium. Collectively, these data demonstrate the relevance of threonine catabolism in T. cruzi metabolism and provide a set of tools to further investigate TcTDH as a potential drug target for Chagas disease.


  • Organizational Affiliation
    • Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Sao Paulo, Brazil.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-threonine 3-dehydrogenase
A, B
366Trypanosoma cruziMutation(s): 0 
Gene Names: Tc00.1047053507923.10
EC: 1.1.1.103
UniProt
Find proteins for Q4CU39 (Trypanosoma cruzi (strain CL Brener))
Explore Q4CU39 
Go to UniProtKB:  Q4CU39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4CU39
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.685α = 90
b = 81.834β = 90.546
c = 83.674γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2018/22202-8
Sao Paulo Research Foundation (FAPESP)Brazil2021/14741-9

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references, Structure summary