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 10ZG | pdb_000010zg

Novobiocin Glycosyltransferase (Ngt-1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.205 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

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

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Ngt-1: A glycosyltransferase that confers resistance to three distinct antibiotic classes.

Abbas, A., Sychantha, D., Koteva, K., Chiao, M., Sokaribo, A., Hackenberger, D., Andres, S., Wright, G.D.

(2026) J Biol Chem 302: 111479-111479

  • DOI: https://doi.org/10.1016/j.jbc.2026.111479
  • Primary Citation Related Structures: 
    10ZG

  • PubMed Abstract: 

    Environmental microbes are a rich source of antibiotic resistance genes with the potential to be mobilized and captured by pathogens under selective pressure. This largely unexplored resistome offers an opportunity to identify novel resistance mechanisms that may eventually emerge in clinical settings, supporting efforts to maintain current antibiotic efficacy. From a screen of environmental bacterial isolates, we identified Bacillus thuringiensis WAC10774 B, which confers resistance to the aminocoumarin antibiotic novobiocin through enzymatic inactivation. Analysis of the inactive antibiotic revealed that WAC10774 B modifies novobiocin via glycosylation, a unique transformation not reported since the antibiotic's discovery 70 years ago. Using activity-guided protein purification, we identified the novobiocin glycosyltransferase, Ngt-1, and its encoding gene. Surprisingly, ngt-1 confers resistance to three structurally distinct antibiotic classes: novobiocin (aminocoumarin), fidaxomicin (tiacumicin), and salinomycin (polyether). To further explore Ngt-1's functional breadth, we performed steady-state kinetic and protein-structure studies, revealing Ngt-1 as a novel, broad-spectrum glycosyltransferase capable of inactivating antibiotics. These findings highlight the importance of exploring the environmental resistome to identify new resistance enzymes and to inform strategies to combat antimicrobial resistance.


  • Organizational Affiliation: 
    • Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.

Macromolecule Content 

  • Total Structure Weight: 47.59 kDa 
  • Atom Count: 3,336 
  • Modeled Residue Count: 370 
  • Deposited Residue Count: 398 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycosyl transferase398Bacillus thuringiensisMutation(s): 0 
Gene Names: BK741_28350
UniProt
Find proteins for A0A1W6WLH5 (Bacillus thuringiensis)
Explore A0A1W6WLH5 
Go to UniProtKB:  A0A1W6WLH5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W6WLH5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.029α = 90
b = 95.219β = 90
c = 102.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT183745

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-06
    Type: Initial release
  • Version 1.1: 2026-06-03
    Changes: Database references