9HJW | pdb_00009hjw

Crystal structure of flavin-dependent monooxygenase Tet(X4) in complex with tegaserod


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.209 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Binding assays enable discovery of Tet(X) inhibitors that combat tetracycline destructase resistance.

Beech, M.J.Toma, E.C.Smith, H.G.Trush, M.M.Ang, J.H.J.Wong, M.Y.Wong, C.H.J.Ali, H.S.Butt, Z.Goel, V.Duarte, F.Farley, A.J.M.Walsh, T.R.Schofield, C.J.

(2025) Chem Sci 16: 9691-9704

  • DOI: https://doi.org/10.1039/d5sc00964b
  • Primary Citation of Related Structures:  
    9HJV, 9HJW, 9HKE

  • PubMed Abstract: 

    The Tet(X) flavin-dependent monooxygenases enable tetracycline antibiotic resistance by catalysing inactivating hydroxylation, so preventing inhibition of bacterial ribosomes. Tet(X) resistance is growing rapidly, threatening the efficacy of important last-resort tetracyclines such as tigecycline. Tet(X) inhibitors have potential to protect tetracyclines in combination therapies, but their discovery has been hampered by lack of high-throughput assays. We report the development of an efficient fluorescence polarisation Tet(X) binding assay employing a tetramethylrhodamine-glycyl-minocycline conjugate that enables inhibitor discovery. The assay was applied to tetracycline substrates and reported inhibitors, providing insight into their binding modes. Screening of a bioactive molecule library identified novel Tet(X) inhibitors, including psychoactive phenothiazine derivatives and the 5-HT 4 agonist tegaserod, the activities of which were validated by turnover assays. Crystallographic studies of Tet(X4)-inhibitor complexes reveal two new inhibitor binding modes, importantly providing evidence for active site binding of Tet(X) inhibitors that do not share structural similarity with tetracycline substrates. In some cases, potentiation of tigecycline activity was observed in bacteria expressing Tet(X4). The combined results provide non-tetracycline scaffolds for development of potent Tet(X) inhibitors and highlight the need to evaluate the impact of non-antibiotics on antimicrobial resistance.


  • Organizational Affiliation

    Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford Oxford OX1 3TA UK christopher.schofield@chem.ox.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavin-dependent monooxygenase371Escherichia coliMutation(s): 0 
Gene Names: mtr-1
EC: 1.14.13
UniProt
Find proteins for A0A3T0V9Y5 (Escherichia coli)
Explore A0A3T0V9Y5 
Go to UniProtKB:  A0A3T0V9Y5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3T0V9Y5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.209 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.286α = 90
b = 97.286β = 90
c = 167.673γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateIneos Oxford Institute Core Grant

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Database references