7EYT

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF with andilesin C and NOG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Molecular insights into the unusually promiscuous and catalytically versatile Fe(II)/ alpha-ketoglutarate-dependent oxygenase SptF.

Tao, H.Mori, T.Chen, H.Lyu, S.Nonoyama, A.Lee, S.Abe, I.

(2022) Nat Commun 13: 95-95

  • DOI: https://doi.org/10.1038/s41467-021-27636-3
  • Primary Citation of Related Structures:  
    7EYR, 7EYS, 7EYT, 7EYU, 7EYW, 7FCB

  • PubMed Abstract: 

    Non-heme iron and α-ketoglutarate-dependent (Fe/αKG) oxygenases catalyze various oxidative biotransformations. Due to their catalytic flexibility and high efficiency, Fe/αKG oxygenases have attracted keen attention for their application as biocatalysts. Here, we report the biochemical and structural characterizations of the unusually promiscuous and catalytically versatile Fe/αKG oxygenase SptF, involved in the biosynthesis of fungal meroterpenoid emervaridones. The in vitro analysis revealed that SptF catalyzes several continuous oxidation reactions, including hydroxylation, desaturation, epoxidation, and skeletal rearrangement. SptF exhibits extremely broad substrate specificity toward various meroterpenoids, and efficiently produced unique cyclopropane-ring-fused 5/3/5/5/6/6 and 5/3/6/6/6 scaffolds from terretonins. Moreover, SptF also hydroxylates steroids, including androsterone, testosterone, and progesterone, with different regiospecificities. Crystallographic and structure-based mutagenesis studies of SptF revealed the molecular basis of the enzyme reactions, and suggested that the malleability of the loop region contributes to the remarkable substrate promiscuity. SptF exhibits great potential as a promising biocatalyst for oxidation reactions.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-oxoglutarate/Fe(II)-dependent dioxygenase SptFA [auth C],
B [auth A],
C [auth B],
D
296Aspergillus sp.Mutation(s): 0 
Gene Names: sptF
UniProt
Find proteins for A0A6J4CX17 (Aspergillus sp)
Explore A0A6J4CX17 
Go to UniProtKB:  A0A6J4CX17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6J4CX17
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.054α = 81.739
b = 72.557β = 84.189
c = 78.826γ = 70.229
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description