9F5V | pdb_00009f5v

Crystal structure of thiol peroxidase from Helicobacter pylori (HpTx, reduced)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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 

  • 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.


  • Organizational Affiliation
    • TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies, Technical University Munich, Garching, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiol peroxidase
A, B
188Helicobacter pyloriMutation(s): 0 
Gene Names: tpxHP_0390
EC: 1.11.1.24
UniProt
Find proteins for O25151 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25151 
Go to UniProtKB:  O25151
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25151
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.53α = 90
b = 68.63β = 98.96
c = 64.38γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB 1309 - 325871075

Revision History  (Full details and data files)

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