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- EMDB-39557: Helicobacter pylori OorDABC in complex with Napabucasin -

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Basic information

Entry
Database: EMDB / ID: EMD-39557
TitleHelicobacter pylori OorDABC in complex with Napabucasin
Map data
Sample
  • Complex: Helicobacter pylori OorDABC in complex with Napabucasin
    • Protein or peptide: 2-oxoglutarate:acceptor oxidoreductase
    • Protein or peptide: 2-oxoglutarate synthase subunit alpha
    • Protein or peptide: 2-oxoglutarate ferredoxin oxidoreductase subunit beta
    • Protein or peptide: 2-oxoglutarate:acceptor oxidoreductase
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Napabucasin
  • Ligand: MAGNESIUM ION
  • Ligand: THIAMINE DIPHOSPHATE
KeywordsOxoglutarate Oxidoreductase / Electron Transport / Tricarboxylic Acid Cycle / Napabucasin / OXIDOREDUCTASE
Function / homology
Function and homology information


2-oxoglutarate synthase activity / small molecule metabolic process / thiamine pyrophosphate binding
Similarity search - Function
: / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
2-oxoglutarate ferredoxin oxidoreductase subunit beta / : / : / :
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsLan W / Gao Y / Bi H
Funding support China, 7 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073899 China
National Natural Science Foundation of China (NSFC)31570053 China
National Natural Science Foundation of China (NSFC)31870029 China
National Natural Science Foundation of China (NSFC)82302542 China
The National Key Research and Development Program of China2018YFC0311003
The National Key Research and Development Program of China2022YFA1305900
Shanghai Rising-Star Program23QA1406400
CitationJournal: Nat Commun / Year: 2025
Title: 2-oxoglutarate:acceptor oxidoreductase-catalyzed redox cycling effectively targets coccoid forms of Helicobacter pylori.
Authors: Xudong Hang / Weiqi Lan / Huang Yanqiang / Hongming Huang / Mingjing Zhang / Liping Zeng / Ting Shi / Yuefan Bai / Zhiyu Yang / Shanwei Hu / Junfan Wang / Linlin Dong / Qian Tong / Jia Jia / ...Authors: Xudong Hang / Weiqi Lan / Huang Yanqiang / Hongming Huang / Mingjing Zhang / Liping Zeng / Ting Shi / Yuefan Bai / Zhiyu Yang / Shanwei Hu / Junfan Wang / Linlin Dong / Qian Tong / Jia Jia / Shuzhuang Bi / Qianfeng Xia / Yan Gao / Hongkai Bi /
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. ...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.
History
DepositionMar 22, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39557.png

Downloads & links

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Map

FileDownload / File: emd_39557.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.179
Minimum - Maximum-2.6091433 - 3.886136
Average (Standard dev.)-0.0007340298 (±0.09877919)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39557_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39557_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helicobacter pylori OorDABC in complex with Napabucasin

EntireName: Helicobacter pylori OorDABC in complex with Napabucasin
Components
  • Complex: Helicobacter pylori OorDABC in complex with Napabucasin
    • Protein or peptide: 2-oxoglutarate:acceptor oxidoreductase
    • Protein or peptide: 2-oxoglutarate synthase subunit alpha
    • Protein or peptide: 2-oxoglutarate ferredoxin oxidoreductase subunit beta
    • Protein or peptide: 2-oxoglutarate:acceptor oxidoreductase
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Napabucasin
  • Ligand: MAGNESIUM ION
  • Ligand: THIAMINE DIPHOSPHATE

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Supramolecule #1: Helicobacter pylori OorDABC in complex with Napabucasin

SupramoleculeName: Helicobacter pylori OorDABC in complex with Napabucasin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Helicobacter pylori (bacteria)

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Macromolecule #1: 2-oxoglutarate:acceptor oxidoreductase

MacromoleculeName: 2-oxoglutarate:acceptor oxidoreductase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 12.467625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKMSTPDGV AVWVNEDRCK GCDICVSVCP AGVLGMGIEK ERVLGKVAKV AYPESCIGCV QCELHCPDFA IYVADRKDFK FAKVSKEAQ ERSEKVKANK YMLLEETILE GRGK

UniProtKB: UNIPROTKB: A0A0B2EGL0

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Macromolecule #2: 2-oxoglutarate synthase subunit alpha

MacromoleculeName: 2-oxoglutarate synthase subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 41.565902 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MREIISDGNE LVAKAAIEVG CRFFGGYPIT PSSDIMHAMS VALPKCGGHF IQMEDEISGI SVSLGASMSG TKSMTASSGP GISLKVEQI GYSFMAEIPL VIADVMRSGP STGMPTRVAQ GDVNFLKHPI HGDFKAVALA PASLEEAYTE TVRAFNLAEM L MTPVFLLM ...String:
MREIISDGNE LVAKAAIEVG CRFFGGYPIT PSSDIMHAMS VALPKCGGHF IQMEDEISGI SVSLGASMSG TKSMTASSGP GISLKVEQI GYSFMAEIPL VIADVMRSGP STGMPTRVAQ GDVNFLKHPI HGDFKAVALA PASLEEAYTE TVRAFNLAEM L MTPVFLLM DETVGHMYGK VQIPDLEEVQ KMTINRKEFV GDKKDYKPYG VAQDEPAVLN PFFKGYRYHV SGLHHGPIGF PT EDAKIGG DLIDRLFHKI ESKQDIINEN EEMDLEGAEI VIIAYGSVSL AVKEALKDYH KESKQKVGFF RPKTLWPSPA KRL KEIGDK YEKILVIELN KGQYLEEIER AMQRKVHFFG QANGRTISPK QIIAKLKEL

UniProtKB: UNIPROTKB: A0A2T6W5S4

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Macromolecule #3: 2-oxoglutarate ferredoxin oxidoreductase subunit beta

MacromoleculeName: 2-oxoglutarate ferredoxin oxidoreductase subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: 2-oxoglutarate synthase
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 30.481701 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAFNYDEYLR VDKIPTLWCW GCGDGVILKS IIRTIDALGW KMDDVCLVSG IGCSGRMSSY VNCNTVHTTH GRAVAYATGI KMANPSKHV IVVSGDGDGF AIGGNHTMHA CRRNIDLNFI LVNNFIYGLT NSQTSPTTPN GMWTVTAQWG NIDNQFDPCA L TTAAGASF ...String:
MAFNYDEYLR VDKIPTLWCW GCGDGVILKS IIRTIDALGW KMDDVCLVSG IGCSGRMSSY VNCNTVHTTH GRAVAYATGI KMANPSKHV IVVSGDGDGF AIGGNHTMHA CRRNIDLNFI LVNNFIYGLT NSQTSPTTPN GMWTVTAQWG NIDNQFDPCA L TTAAGASF VARESVLDPQ KLEKVLKEGF SHKGFSFFDV HSNCHINLGR KNKMGEASQM LKWMESRLVS KRQFEAMSPE ER VDKFPTG VLRHDTDRKE YCEAYQEIIE KAQGKQ

UniProtKB: 2-oxoglutarate ferredoxin oxidoreductase subunit beta

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Macromolecule #4: 2-oxoglutarate:acceptor oxidoreductase

MacromoleculeName: 2-oxoglutarate:acceptor oxidoreductase / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 20.253453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEAQLRFTGV GGQGVLLAGE ILAEAKIVSG GYGTKTSTYT SQVRGGPTKV DILLDKDEII FPYAKEGEID FMLSVAQISY NQFKSDIKQ GGIVVIDPNL VTPTKEDEEK YQIYKIPIIS IAKDEVGNII TQSVVALAIT VELTKCVEEN IVLDTMLKKV P AKVADTNK KAFEIGKKHA LEALKVRA

UniProtKB: UNIPROTKB: A0A0B2EEZ8

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 6 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #6: Napabucasin

MacromoleculeName: Napabucasin / type: ligand / ID: 6 / Number of copies: 2 / Formula: A1D65
Molecular weightTheoretical: 240.211 Da

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: THIAMINE DIPHOSPHATE

MacromoleculeName: THIAMINE DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 2 / Formula: TPP
Molecular weightTheoretical: 425.314 Da
Chemical component information

ChemComp-TPP:
THIAMINE DIPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146076
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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