8ER0 | pdb_00008er0

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

• PDB DOI: https://doi.org/10.2210/pdb8ER0/pdb

• Classification: OXIDOREDUCTASE/INHIBITOR
• Organism(s): Chryseobacterium oncorhynchi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-11 Released: 2023-04-26 
• Deposition Author(s): Kumar, H., Tolia, N.H.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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

• PubMed: 37062778 
• DOI: https://doi.org/10.1038/s42003-023-04792-4
• Primary Citation 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.

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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.
Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA.
The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA. [e-mail].
Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA. [e-mail].
Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA. [e-mail].
Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA. [e-mail].
Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA. [e-mail].
Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA. [e-mail].
Host-pathogen interaction and structural vaccinology section (HPISV), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA. [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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.72 kDa 
• Atom Count: 6,308 
• Modeled Residue Count: 739 
• Deposited Residue Count: 806 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin-dependent monooxygenase	A, B	403	Chryseobacterium oncorhynchi	Mutation(s): 0  Gene Names: tet(X) EC: 1.14.13
UniProt
Find proteins for A0A316WTJ0 (Chryseobacterium oncorhynchi) Explore A0A316WTJ0  Go to UniProtKB:  A0A316WTJ0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	D [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
TDC (Subject of Investigation/LOI)	C [auth A], E [auth B]	5A,6-ANHYDROTETRACYCLINE C22 H22 N2 O7 CXCVEERYMJZMMM-DOCRCCHOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.086	α = 90
b = 52.212	β = 95.44
c = 94.871	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Kumar, H., Tolia, N.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	2U01AI123394
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Intramural Research Program

Revision History  

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