6L6X

The structure of ScoE with substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 7UCClick on this verticalbar to view detailsBest fitted TARClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Pathway from N-Alkylglycine to Alkylisonitrile Catalyzed by Iron(II) and 2-Oxoglutarate-Dependent Oxygenases.

Chen, T.Y.Chen, J.Tang, Y.Zhou, J.Guo, Y.Chang, W.C.

(2020) Angew Chem Int Ed Engl 59: 7367-7371

  • DOI: https://doi.org/10.1002/anie.201914896
  • Primary Citation of Related Structures:  
    6L6W, 6L6X, 6L86

  • PubMed Abstract: 

    N-alkylisonitrile, a precursor to isonitrile-containing lipopeptides, is biosynthesized by decarboxylation-assisted -N≡C group (isonitrile) formation by using N-alkylglycine as the substrate. This reaction is catalyzed by iron(II) and 2-oxoglutarate (Fe/2OG) dependent enzymes. Distinct from typical oxygenation or halogenation reactions catalyzed by this class of enzymes, installation of the isonitrile group represents a novel reaction type for Fe/2OG enzymes that involves a four-electron oxidative process. Reported here is a plausible mechanism of three Fe/2OG enzymes, Sav607, ScoE and SfaA, which catalyze isonitrile formation. The X-ray structures of iron-loaded ScoE in complex with its substrate and the intermediate, along with biochemical and biophysical data reveal that -N≡C bond formation involves two cycles of Fe/2OG enzyme catalysis. The reaction starts with an Fe IV -oxo-catalyzed hydroxylation. It is likely followed by decarboxylation-assisted desaturation to complete isonitrile installation.


  • Organizational Affiliation

    Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ScoE protein346Streptomyces coeruleorubidusMutation(s): 0 
Gene Names: ScoE
EC: 1.14.11.78
UniProt
Find proteins for A0A3B6UEU3 (Streptomyces coeruleorubidus)
Explore A0A3B6UEU3 
Go to UniProtKB:  A0A3B6UEU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3B6UEU3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.2α = 90
b = 97.2β = 90
c = 70.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 7UCClick on this verticalbar to view detailsBest fitted TARClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description