6L86

The structure of SfaA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
Taurine catabolism dioxygenase
A, B, C, D
315Streptomyces thioluteusMutation(s): 0 
UniProt
Find proteins for A0A2H4T920 (Streptomyces thioluteus)
Explore A0A2H4T920 
Go to UniProtKB:  A0A2H4T920
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2H4T920
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLT (Subject of Investigation/LOI)
Query on MLT

Download Ideal Coordinates CCD File 
G [auth A]D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
LMR (Subject of Investigation/LOI)
Query on LMR

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
J [auth B],
L [auth C],
N [auth D]
(2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
M [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.173α = 90
b = 150.173β = 90
c = 387.859γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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