7ZHZ

Leishmania donovani Glucose 6-Phosphate Dehydrogenase mutant C138S complexed with G6P and NADP(H)

PDB DOI: https://doi.org/10.2210/pdb7ZHZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leishmania donovani
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-04-07 Released: 2022-12-14
Deposition Author(s): Fritz-Wolf, K., Berneburg, I.
Funding Organization(s): LOEWE Center DRUID (Novel Drug Targets against Poverty-related and Neglected Tropical Infectious Diseases)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.298
R-Value Work: 0.249
R-Value Observed: 0.254

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s42003-022-04307-7
Primary Citation of 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.

Organizational Affiliation

Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany.

Macromolecule Content

Total Structure Weight: 129.46 kDa
Atom Count: 8,532
Modelled Residue Count: 1,055
Deposited Residue Count: 1,124
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate 1-dehydrogenase	A, B	562	Leishmania donovani	Mutation(s): 1 Gene Names: g6pdh EC: 1.1.1.49
UniProt
Find proteins for A2CIL3 (Leishmania donovani) Explore A2CIL3 Go to UniProtKB: A2CIL3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2CIL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
BG6 (Subject of Investigation/LOI) Query on BG6 Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	6-O-phosphono-beta-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-VFUOTHLCSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	F [auth A] G [auth A] H [auth A] M [auth B] N [auth B] F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B]	D [auth A], E [auth A], I [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth B]