8C79 | pdb_00008c79

Crystal structure of Leishmania donovani 6-Phosphogluconate Dehydrogenase complexed with NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.317 (Depositor), 0.317 (DCC) 
  • R-Value Work: 
    0.262 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure of Leishmania donovani 6-Phosphogluconate Dehydrogenase and Inhibition by Phosphine Gold(I) Complexes: A Potential Approach to Leishmaniasis Treatment.

Berneburg, I.Stumpf, M.Velten, A.S.Rahlfs, S.Przyborski, J.Becker, K.Fritz-Wolf, K.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24108615
  • Primary Citation Related Structures: 
    8C79

  • PubMed Abstract: 

    As unicellular parasites are highly dependent on NADPH as a source for reducing equivalents, the main NADPH-producing enzymes glucose 6-phosphate dehydrogenase (G6PD) and 6-phosphogluconate dehydrogenase (6PGD) of the pentose phosphate pathway are considered promising antitrypanosomatid drug targets. Here we present the biochemical characterization and crystal structure of Leishmania donovani 6PGD ( Ld 6PGD) in complex with NADP(H). Most interestingly, a previously unknown conformation of NADPH is visible in this structure. In addition, we identified auranofin and other gold(I)-containing compounds as efficient Ld 6PGD inhibitors, although it has so far been assumed that trypanothione reductase is the sole target of auranofin in Kinetoplastida . Interestingly, 6PGD from Plasmodium falciparum is also inhibited at lower micromolar concentrations, whereas human 6PGD is not. Mode-of-inhibition studies indicate that auranofin competes with 6PG for its binding site followed by a rapid irreversible inhibition. By analogy with other enzymes, this suggests that the gold moiety is responsible for the observed inhibition. Taken together, we identified gold(I)-containing compounds as an interesting class of inhibitors against 6PGDs from Leishmania and possibly from other protozoan parasites. Together with the three-dimensional crystal structure, this provides a valid basis for further drug discovery approaches.


  • Organizational Affiliation
    • Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, 35392 Giessen, Germany.

Macromolecule Content 

  • Total Structure Weight: 105.42 kDa 
  • Atom Count: 7,366 
  • Modeled Residue Count: 956 
  • Deposited Residue Count: 956 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
6-phosphogluconate dehydrogenase, decarboxylating
A, B
478Leishmania donovaniMutation(s): 0 
Gene Names: gnd
EC: 1.1.1.44
UniProt
Find proteins for Q18L02 (Leishmania donovani)
Explore Q18L02 
Go to UniProtKB:  Q18L02
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ18L02
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.317 (Depositor), 0.317 (DCC) 
  • R-Value Work:  0.262 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.87α = 90
b = 117.35β = 90
c = 128.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LOEWE Center DRUIDGermanyB3/E3

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description