8ER0

X-ray crystal structure of Tet(X6) bound to anhydrotetracycline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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


Literature

Structure of anhydrotetracycline-bound Tet(X6) reveals the mechanism for inhibition of type 1 tetracycline destructases.

Kumar, H.Williford, E.E.Blake, K.S.Virgin-Downey, B.Dantas, G.Wencewicz, T.A.Tolia, N.H.

(2023) Commun Biol 6: 423-423

  • DOI: https://doi.org/10.1038/s42003-023-04792-4
  • Primary Citation of Related Structures:  
    8ER0, 8ER1

  • PubMed Abstract: 

    Inactivation of tetracycline antibiotics by tetracycline destructases (TDases) remains a clinical and agricultural threat. TDases can be classified as type 1 Tet(X)-like TDases and type 2 soil-derived TDases. Type 1 TDases are widely identified in clinical pathogens. A combination therapy of tetracycline and a TDase inhibitor is much needed to rescue the clinical efficacy of tetracyclines. Anhydrotetracycline is a pan-TDase inhibitor that inhibits both type 1 and type 2 TDases. Here, we present structural, biochemical, and phenotypic evidence that anhydrotetracycline binds in a substrate-like orientation and competitively inhibits the type 1 TDase Tet(X6) to rescue tetracycline antibiotic activity as a sacrificial substrate. Anhydrotetracycline interacting residues of Tet(X6) are conserved within type 1 TDases, indicating a conserved binding mode and mechanism of inhibition. This mode of binding and inhibition is distinct from anhydrotetracycline's inhibition of type 2 TDases. This study forms the framework for development of next-generation therapies to counteract enzymatic tetracycline resistance.


  • Organizational Affiliation

    Host-pathogen interaction and structural vaccinology section (HPISV), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavin-dependent monooxygenase
A, B
403Chryseobacterium oncorhynchiMutation(s): 0 
Gene Names: tet(X)
EC: 1.14.13
UniProt
Find proteins for A0A316WTJ0 (Chryseobacterium oncorhynchi)
Explore A0A316WTJ0 
Go to UniProtKB:  A0A316WTJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A316WTJ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.086α = 90
b = 52.212β = 95.44
c = 94.871γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States2U01AI123394
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesIntramural Research Program

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description