8YS6 | pdb_00008ys6

Helicobacter pylori OorDABC in complex with Napabucasin

  • Classification: OXIDOREDUCTASE
  • Organism(s): Helicobacter pylori
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-03-22 Released: 2025-07-02 
  • Deposition Author(s): Lan, W., Gao, Y., Bi, H.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), The National Key Research and Development Program of China, Shanghai Rising-Star Program

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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


Literature

2-oxoglutarate:acceptor oxidoreductase-catalyzed redox cycling effectively targets coccoid forms of Helicobacter pylori.

Hang, X., Lan, W., Yanqiang, H., Huang, H., Zhang, M., Zeng, L., Shi, T., Bai, Y., Yang, Z., Hu, S., Wang, J., Dong, L., Tong, Q., Jia, J., Bi, S., Xia, Q., Gao, Y., Bi, H.

(2025) Nat Commun 16: 6965-6965

  • DOI: https://doi.org/10.1038/s41467-025-62477-4
  • Primary Citation of Related Structures:  
    8YS5, 8YS6

  • PubMed Abstract: 

    Helicobacter pylori, a globally significant pathogen, plays a central etiological role in diverse gastric pathologies ranging from chronic gastritis and peptic ulcers to gastric adenocarcinoma. Although conventional antibiotics effectively inhibit or kill growing helical H. pylori, metabolically dormant coccoid forms of H. pylori exhibit considerable tolerance, posing a persistent and clinically significant challenge. Here, we report napabucasin (2-acetylfuro-1,4-naphthoquinone) as a redox-cycling antibiotic with potent bactericidal activity against both drug-resistant helical and coccoid forms of H. pylori. Notably, napabucasin does not induce acquired resistance in vitro and demonstrates superior efficacy compared to standard triple therapy in murine infection models. Mechanistic studies reveal that napabucasin acts through 2-oxoglutarate:acceptor oxidoreductase (OOR)-catalyzed futile redox cycling, generating bactericidal levels of reactive oxygen species (ROS). Compared to menaquinone 6, a proposed physiological electron acceptor, napabucasin exhibits enhanced oxidative capacity. Structural, biochemical, and microbiological analyses identify Leu44 and Lys46 within the OorD subunit as critical residues for napabucasin recognition and catalysis. These findings establish OOR-mediated redox cycling as a robust antimicrobial strategy that sustains endogenous ROS production to combat refractory H. pylori infections.

    • Organizational Affiliation: 
    • NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-oxoglutarate:acceptor oxidoreductaseA [auth D],
E [auth F]		113Helicobacter pyloriMutation(s): 0 
Gene Names: AM496_04450, BB411_07145, C2R64_04560, D8X81_03145, DD775_02535, EC515_04135, EC541_05865, EC589_03065, HPY1198_04840, HPY1846_01345
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
2-oxoglutarate synthase subunit alphaB [auth A],
F [auth G]		375Helicobacter pyloriMutation(s): 0 
Gene Names: C2R48_00275
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
2-oxoglutarate ferredoxin oxidoreductase subunit betaC,
G [auth H]		273Helicobacter pyloriMutation(s): 0 
Gene Names: 
oorB, korB, AM497_01150, AM498_01330, B0X30_00560, B0X44_00010, B0X50_03675, B0X54_05595, B0X62_02935, BB411_07135, BB413_05640, BB424_05915, BB459_03745, BB461_04720, BB464_04365, BB477_04855, BB479_06520, BGL55_07715, BGL66_00450, BGL68_05120, BGL69_01465, BGL72_06170, BXP09_03780, C2840_03070, C2R45_06185, C2R60_07105, C2R62_02105, C2R64_04570, C2R66_01600, C2R71_01550, C2R81_00990, C2R85_07970, C2R86_01670, C2R96_02100, C2S01_06600, C2S04_03540, C2S07_06030, C2S08_01675, C2S19_05560, C2S26_01775, C2S41_04370, C2S43_01830, C2S44_08445, CV723_03795, CV726_04550, CV728_03440, CV729_03960, CV730_03830, D2C73_05440, D2C76_08055, D2C79_04285, D2C84_02640, D2C85_05055, D2C87_02355, D8X56_03120, D8X81_03155, DD750_02510, DD754_03015, DD756_02785, DD764_03055, DD775_02545, DD794_03540, DDP37_03580, DDP42_03140, DDP57_02985, EC508_04845, EC515_04145, EC518_06710, EC525_03565, EC532_06000, EC533_02415, EC535_02670, EC538_03525, EC547_02955, EC551_04645, EC553_02910, EC556_02780, EC568_02905, EC569_04000, EC570_04715, EC572_05350, EC574_04050, EC582_05020, EC589_03055, EC595_02590, EC597_01970, EC598_00990, EC600_00880, EC601_02710, ECB88_05740, ECB91_01840, ECC09_04670, ECC11_04890, ECC12_01920, ECC19_03410, ECC24_01145, ECC25_02460, ECC26_02695, ECC33_03050, ECC34_02995, ECC35_03455, ECC43_04085, ECC49_04355, ECE46_02140, EDB75_01155, EDC85_02050, EGW01_04140, EPC67_05165, EPC72_01580, EPC80_01190, F7187_05770, F7198_05900, F7221_03625, F7229_07365, HPPMSS1_c00647, HPY1198_04850, NCTC12823_00718

EC: 1.2.7.3
UniProt
Find proteins for A0A024BZG2 (Helicobacter pylori)
Explore A0A024BZG2 
Go to UniProtKB:  A0A024BZG2
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UniProt GroupA0A024BZG2
Sequence Annotations
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
2-oxoglutarate:acceptor oxidoreductaseD [auth B],
H [auth I]		186Helicobacter pyloriMutation(s): 0 
Gene Names: oorC, C2R64_04575, C2S01_06595, EC570_04720, ECC29_01410, ECC33_03045
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP (Subject of Investigation/LOI)
Query on TPP
Download Ideal Coordinates CCD File 
N [auth C],
T [auth H]		THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
SF4 (Subject of Investigation/LOI)
Query on SF4
Download Ideal Coordinates CCD File 
I [auth D]
J [auth D]
L [auth C]
O [auth F]
P [auth F]
I [auth D],
J [auth D],
L [auth C],
O [auth F],
P [auth F],
R [auth H]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
A1D65 (Subject of Investigation/LOI)
Query on A1D65
Download Ideal Coordinates CCD File 
K [auth D],
Q [auth F]		Napabucasin
C14 H8 O4
DPHUWDIXHNQOSY-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
M [auth C],
S [auth H]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82073899
National Natural Science Foundation of China (NSFC)China31570053
National Natural Science Foundation of China (NSFC)China31870029
National Natural Science Foundation of China (NSFC)China82302542
The National Key Research and Development Program of China2018YFC0311003
The National Key Research and Development Program of China2022YFA1305900
Shanghai Rising-Star Program23QA1406400

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2026-01-21
    Changes: Data collection, Database references