8G5U

Crystal structure of TnmK2 complexed with TNM B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Cofactorless oxygenases guide anthraquinone-fused enediyne biosynthesis.

Gui, C.Kalkreuter, E.Liu, Y.C.Li, G.Steele, A.D.Yang, D.Chang, C.Shen, B.

(2024) Nat Chem Biol 20: 243-250

  • DOI: https://doi.org/10.1038/s41589-023-01476-2
  • Primary Citation of Related Structures:  
    8G5S, 8G5T, 8G5U

  • PubMed Abstract: 

    The anthraquinone-fused enediynes (AFEs) combine an anthraquinone moiety and a ten-membered enediyne core capable of generating a cytotoxic diradical species. AFE cyclization is triggered by opening the F-ring epoxide, which is also the site of the most structural diversity. Previous studies of tiancimycin A, a heavily modified AFE, have revealed a cryptic aldehyde blocking installation of the epoxide, and no unassigned oxidases could be predicted within the tnm biosynthetic gene cluster. Here we identify two consecutively acting cofactorless oxygenases derived from methyltransferase and α/β-hydrolase protein folds, TnmJ and TnmK2, respectively, that are responsible for F-ring tailoring in tiancimycin biosynthesis by comparative genomics. Further biochemical and structural characterizations reveal that the electron-rich AFE anthraquinone moiety assists in catalyzing deformylation, epoxidation and oxidative ring cleavage without exogenous cofactors. These enzymes therefore fill important knowledge gaps for the biosynthesis of this class of molecules and the underappreciated family of cofactorless oxygenases.


  • Organizational Affiliation

    Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TnmK2
A, B, C, D
489Streptomyces sp. CB03234Mutation(s): 0 
Gene Names: tnmK2AMK26_32040
UniProt
Find proteins for A0A125SA15 (Streptomyces sp. (strain CB03234))
Explore A0A125SA15 
Go to UniProtKB:  A0A125SA15
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125SA15
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.11α = 90
b = 134.11β = 90
c = 355.757γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data 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 General Medical Sciences (NIH/NIGMS)United StatesGM134954

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Database references
  • Version 1.2: 2024-02-14
    Changes: Database references