5AQ1 | pdb_00005aq1

Trypanosoma cruzi Glucose-6-phosphate Dehydrogenase in complex with G6P and NADPH

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.226 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

The Structure of a Trypanosoma Cruzi Glucose-6-Phosphate Dehydrogenase Reveals Differences from the Mammalian Enzyme.

Mercaldi, G.F., Dawson, A., Hunter, W.N., Cordeiro, A.T.

(2016) FEBS Lett 590: 2776

  • DOI: https://doi.org/10.1002/1873-3468.12276
  • Primary Citation Related Structures: 
    5AQ1

  • PubMed Abstract: 

    The enzyme glucose-6-phosphate dehydrogenase from Trypanosoma cruzi (TcG6PDH) catalyses the first step of the pentose phosphate pathway (PPP) and is considered a promising target for the discovery of a new drug against Chagas diseases. In the present work, we describe the crystal structure of TcG6PDH obtained in a ternary complex with the substrate β-d-glucose-6-phosphate (G6P) and the reduced 'catalytic' cofactor NADPH, which reveals the molecular basis of substrate and cofactor recognition. A comparison with the homologous human protein sheds light on differences in the cofactor-binding site that might be explored towards the design of new NADP(+) competitive inhibitors targeting the parasite enzyme.

    • Organizational Affiliation: 
    • Brazilian Biosciences National Laboratory, Center of Research in Energy and Materials, Campinas, Brazil.

Macromolecule Content 

  • Total Structure Weight: 175.88 kDa 
  • Atom Count: 12,016 
  • Modeled Residue Count: 1,452 
  • Deposited Residue Count: 1,527 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUCOSE-6-PHOSPHATE DEHYDROGENASE
A, B, C
509Trypanosoma cruziMutation(s): 0 
EC: 1.1.1.49
UniProt
Find proteins for Q4E0B2 (Trypanosoma cruzi (strain CL Brener))
Explore Q4E0B2 
Go to UniProtKB:  Q4E0B2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4E0B2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.226 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.946α = 90
b = 154.946β = 90
c = 348.358γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-09-28
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-06
    Changes: Structure summary