9F64 | pdb_00009f64

Crystal structure of thiol peroxidase mutant (C94A) in complex with Metro* (H. pylori

• PDB DOI: https://doi.org/10.2210/pdb9F64/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-04-30 Released: 2025-05-14 
• Deposition Author(s): Fiedler, M.K., Gong, R., Fuchs, S., Rox, K., Friedrich, V., Pfeiffer, D., Reinhardt, T., Mibus, C., Huber, M., Hess, C., Mejias-Luque, R., Gerhard, M., Groll, M., Sieber, S.A.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Metronidazole and ether derivatives target Helicobacter pylori via simultaneous stress induction and inhibition.

Fiedler, M.K., Pandler, M.S.I., Gong, R., Fuchs, S., Rox, K., Friedrich, V., Pfeiffer, D., Singh, D., Reinhardt, T., Mibus, C., Huber, M., Hess, C.R., Mejias-Luque, R., Gerhard, M., Groll, M., Sieber, S.A.

(2026) Nat Microbiol 11: 1049-1063

• PubMed: 41851492 
• DOI: https://doi.org/10.1038/s41564-026-02291-w
• Primary Citation Related Structures: 
  9F5V, 9F64, 9F65


• PubMed Abstract: 
  

  Metronidazole is a front-line drug for the treatment of Helicobacter pylori infections. However, its mode of action and cellular targets are poorly defined, and higher dosing and combination therapies are required to overcome resistance. Here we performed activity-based protein profiling with tailored metronidazole probes and identified chaperonin HpGroEL and thiol peroxidase HpTpx as prominent targets, the latter being essential for H. pylori survival under oxidative stress. Alkynylated ether probes exhibited enhanced antibacterial potency compared with the parent drug in vitro, including activity against resistant strains. Biological assays, chemical proteomics and co-crystallization studies confirmed target engagement, with enhanced binding of ether derivatives to HpTpx. Refined ether analogues exhibited favourable pharmacological profiles without cytotoxicity. The in vivo activity of ether analogues using an H. pylori mouse model demonstrated full bacterial eradication at low dosing of 0.3 mg kg ^-1  day ^-1 . Our findings reveal that stress induction and simultaneous inhibition of the stress response represent a mechanism of this compound class.

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Organizational Affiliation: 
• TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies, Technical University Munich, Garching, Germany.
TUM School of Medicine and Health, Department Preclinical Medicine, Institute of Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany.
German Center for Infection Research, Partner Site Munich, Munich, Germany.
Department of Pediatric Gastroenterology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
German Center for Infection Research, Partner Site Hannover-Braunschweig, Braunschweig, Germany.
TUM School of Natural Sciences, Department of Chemistry, Catalysis Research Center, Technical University of Munich, Garching, Germany.
Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg, Germany.
TUM School of Natural Sciences, Department Biosciences, Chair of Biochemistry, Center for Functional Protein Assemblies, Technical University Munich, Garching, Germany.
TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies, Technical University Munich, Garching, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.93 kDa 
• Atom Count: 1,330 
• Modeled Residue Count: 165 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol peroxidase	A	188	Helicobacter pylori	Mutation(s): 1  Gene Names: tpx, HP_0390 EC: 1.11.1.24
UniProt
Find proteins for O25151 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25151  Go to UniProtKB:  O25151

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IAQ (Subject of Investigation/LOI)	B [auth A]	2-(5-azanyl-2-methyl-imidazol-1-yl)ethanol C6 H11 N3 O QIXFXNMDRJRTIJ-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.37	α = 90
b = 71.48	β = 115.91
c = 40.77	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Fiedler, M.K., Gong, R., Fuchs, S., Rox, K., Friedrich, V., Pfeiffer, D., Reinhardt, T., Mibus, C., Huber, M., Hess, C., Mejias-Luque, R., Gerhard, M., Groll, M., Sieber, S.A.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 1309 - 325871075

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release
  
• Version 1.1: 2026-04-08
  Changes: Database references
• Version 1.2: 2026-04-22
  Changes: Database references