5AQ1

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

• PDB DOI: https://doi.org/10.2210/pdb5AQ1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-18 Released: 2016-07-20 
• Deposition Author(s): Mercaldi, G.F., Dawson, A., Hunter, W.N., Cordeiro, A.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.226 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Starting Model: experimental

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

• PubMed: 27391210 
• DOI: https://doi.org/10.1002/1873-3468.12276
• Primary Citation of 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.

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Organizational Affiliation: 

Brazilian Biosciences National Laboratory, Center of Research in Energy and Materials, Campinas, Brazil.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSE-6-PHOSPHATE DEHYDROGENASE	A, B, C	509	Trypanosoma cruzi	Mutation(s): 0  EC: 1.1.1.49
UniProt
Find proteins for Q4E0B2 (Trypanosoma cruzi (strain CL Brener)) Explore Q4E0B2  Go to UniProtKB:  Q4E0B2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	E [auth A], G [auth B], I [auth C]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
BG6	D [auth A], F [auth B], H [auth C]	6-O-phosphono-beta-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-VFUOTHLCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.226 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.946	α = 90
b = 154.946	β = 90
c = 348.358	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Mercaldi, G.F., Dawson, A., Hunter, W.N., Cordeiro, A.T.

Revision History  

• 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