5TUM

Crystal structure of tetracycline destructase Tet(56)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Plasticity, dynamics, and inhibition of emerging tetracycline resistance enzymes.

Park, J.Gasparrini, A.J.Reck, M.R.Symister, C.T.Elliott, J.L.Vogel, J.P.Wencewicz, T.A.Dantas, G.Tolia, N.H.

(2017) Nat Chem Biol 13: 730-736

  • DOI: https://doi.org/10.1038/nchembio.2376
  • Primary Citation of Related Structures:  
    5TUE, 5TUF, 5TUI, 5TUK, 5TUL, 5TUM

  • PubMed Abstract: 

    Although tetracyclines are an important class of antibiotics for use in agriculture and the clinic, their efficacy is threatened by increasing resistance. Resistance to tetracyclines can occur through efflux, ribosomal protection, or enzymatic inactivation. Surprisingly, tetracycline enzymatic inactivation has remained largely unexplored, despite providing the distinct advantage of antibiotic clearance. The tetracycline destructases are a recently discovered family of tetracycline-inactivating flavoenzymes from pathogens and soil metagenomes that have a high potential for broad dissemination. Here, we show that tetracycline destructases accommodate tetracycline-class antibiotics in diverse and novel orientations for catalysis, and antibiotic binding drives unprecedented structural dynamics facilitating tetracycline inactivation. We identify a key inhibitor binding mode that locks the flavin adenine dinucleotide cofactor in an inactive state, functionally rescuing tetracycline activity. Our results reveal the potential of a new tetracycline and tetracycline destructase inhibitor combination therapy strategy to overcome resistance by enzymatic inactivation and restore the use of an important class of antibiotics.


  • Organizational Affiliation

    Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tetracycline destructase Tet(56)
A, B
410Legionella longbeachaeMutation(s): 0 
Gene Names: LLO_2673
EC: 1.14.13
UniProt
Find proteins for D3HKY4 (Legionella longbeachae serogroup 1 (strain NSW150))
Explore D3HKY4 
Go to UniProtKB:  D3HKY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3HKY4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.45α = 90
b = 114.01β = 90
c = 94.84γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



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 States1R01AI123394-01

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references
  • Version 1.2: 2017-07-05
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-06
    Changes: Data collection, Database references