2WDW

The Native Crystal Structure of the Primary Hexose Oxidase (Dbv29) in Antibiotic A40926 Biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Interception of Teicoplanin Oxidation Intermediates Yields New Antimicrobial Scaffolds

Liu, Y.-C.Li, Y.-S.Lyu, S.-Y.Hsu, L.-J.Chen, Y.-H.Huang, Y.-T.Chan, H.-C.Huang, C.-J.Chen, G.-H.Chou, C.-C.Tsai, M.-D.Li, T.-L.

(2011) Nat Chem Biol 7: 304

  • DOI: https://doi.org/10.1038/nchembio.556
  • Primary Citation of Related Structures:  
    2WDW, 5AWV

  • PubMed Abstract: 

    In the search for new efficacious antibiotics, biosynthetic engineering offers attractive opportunities to introduce minor alterations to antibiotic structures that may overcome resistance. Dbv29, a flavin-containing oxidase, catalyzes the four-electron oxidation of a vancomycin-like glycopeptide to yield A40926. Structural and biochemical examination of Dbv29 now provides insights into residues that govern flavinylation and activity, protein conformation and reaction mechanism. In particular, the serendipitous discovery of a reaction intermediate in the crystal structure led us to identify an unexpected opportunity to intercept the normal enzyme mechanism at two different points to create new teicoplanin analogs. Using this method, we synthesized families of antibiotic analogs with amidated and aminated lipid chains, some of which showed marked potency and efficacy against multidrug resistant pathogens. This method offers a new strategy for the development of chemical diversity to combat antibacterial resistance.


  • Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE HEXOSE OXIDASE
A, B
523Nonomuraea gerenzanensisMutation(s): 0 
EC: 1.1.3.13
UniProt
Find proteins for Q7WZ62 (Nonomuraea gerenzanensis)
Explore Q7WZ62 
Go to UniProtKB:  Q7WZ62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7WZ62
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.092α = 90
b = 66.092β = 90
c = 790.462γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary