7ZHY | pdb_00007zhy

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

PDB DOI: https://doi.org/10.2210/pdb7ZHY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leishmania donovani
Expression System: Escherichia coli BL21(DE3)
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: 1.99 Å
R-Value Free:
0.219 (Depositor), 0.215 (DCC)
R-Value Work:
0.183 (Depositor)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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 PubMed Search on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 131.37 kDa
Atom Count: 9,522
Modeled Residue Count: 1,062
Deposited Residue Count: 1,124
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A2CIL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 X [auth B] MOL2 format, chain C [auth A] MOL2 format, chain X [auth B] mmCIF format, chain C [auth A] mmCIF format, chain X [auth B]	C [auth A], X [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain X [auth B] Interactions & Density Focus chain C [auth A] Focus chain X [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth B] SDF format, chain G [auth A] SDF format, chain EA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain EA [auth B]	EA [auth B], G [auth A], HA [auth B], I [auth A], M [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain G [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain M [auth A] Interactions & Density Focus chain EA [auth B] Focus chain G [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain M [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain Z [auth B] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain SA [auth B] SDF format, chain E [auth A] SDF format, chain CA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth B]	CA [auth B] E [auth A] SA [auth B] T [auth A] U [auth A] CA [auth B], E [auth A], SA [auth B], T [auth A], U [auth A], V [auth A], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth B] Focus chain E [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth B] Focus chain E [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain Y [auth B] SDF format, chain W [auth B] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain H [auth A] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain DA [auth B] SDF format, chain D [auth A] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth B] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth B] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] D [auth A] DA [auth B] F [auth A] AA [auth B], BA [auth B], D [auth A], DA [auth B], F [auth A], FA [auth B], GA [auth B], H [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], W [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain H [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain W [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain H [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain W [auth B] Focus chain Y [auth B]