7ZHT | pdb_00007zht

Leishmania donovani Glucose 6-Phosphate Dehydrogenase apo form

• PDB DOI: https://doi.org/10.2210/pdb7ZHT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Leishmania donovani
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-04-07 Released: 2022-12-14 
• Deposition Author(s): Fritz-Wolf, K., Berneburg, I.
• Funding Organization(s): LOEWE Center DRUID (Project B3 and E3) within the Hessian Excellence Program

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.304 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Leishmania donovani glucose 6-phosphate dehydrogenase reveals a unique N-terminal domain.

Berneburg, I., Rahlfs, S., Becker, K., Fritz-Wolf, K.

(2022) Commun Biol 5: 1353-1353

• PubMed: 36494598 
• DOI: https://doi.org/10.1038/s42003-022-04307-7
• Primary Citation Related Structures: 
  7ZHT, 7ZHU, 7ZHV, 7ZHW, 7ZHX, 7ZHY, 7ZHZ


• PubMed Abstract: 
  

  Since unicellular parasites highly depend on NADPH as a source for reducing equivalents, the pentose phosphate pathway, especially the first and rate-limiting NADPH-producing enzyme glucose 6-phosphate dehydrogenase (G6PD), is considered an excellent antitrypanosomatid drug target. Here we present the crystal structure of Leishmania donovani G6PD (LdG6PD) elucidating the unique N-terminal domain of Kinetoplastida G6PDs. Our investigations on the function of the N-domain suggest its involvement in the formation of a tetramer that is completely different from related Trypanosoma G6PDs. Structural and functional investigations further provide interesting insights into the binding mode of LdG6PD, following an ordered mechanism, which is confirmed by a G6P-induced domain shift and rotation of the helical N-domain. Taken together, these insights into LdG6PD contribute to the understanding of G6PDs' molecular mechanisms and provide an excellent basis for further drug discovery approaches.

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Organizational Affiliation: 
• Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany.
Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany. [e-mail].
Max Planck Institute for Medical Research, Heidelberg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 254.48 kDa 
• Atom Count: 16,104 
• Modeled Residue Count: 2,023 
• Deposited Residue Count: 2,248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate 1-dehydrogenase	A, B, C, D	562	Leishmania donovani	Mutation(s): 0  Gene Names: g6pdh EC: 1.1.1.49
UniProt
Find proteins for A2CIL3 (Leishmania donovani) Explore A2CIL3  Go to UniProtKB:  A2CIL3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], K [auth B], O [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], M [auth C], N [auth C], P [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.304 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.69	α = 90
b = 65.82	β = 92.35
c = 189.22	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-14 
Deposition Author(s): Fritz-Wolf, K., Berneburg, I.

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Funding Organization	Location	Grant Number
LOEWE Center DRUID (Project B3 and E3) within the Hessian Excellence Program	Germany	Project B3 and E3

Revision History  

• Version 1.0: 2022-12-14
  Type: Initial release
  
• Version 1.1: 2022-12-21
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.3: 2025-10-01
  Changes: Advisory, Derived calculations, Structure summary