4XLO

Crystal Structure of EncM (crystallized with 4 mM NADPH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement.

Teufel, R.Miyanaga, A.Michaudel, Q.Stull, F.Louie, G.Noel, J.P.Baran, P.S.Palfey, B.Moore, B.S.

(2013) Nature 503: 552-556

  • DOI: 10.1038/nature12643
  • Primary Citation of Related Structures:  
  • Also Cited By: 4XLO

  • PubMed Abstract: 
  • Flavoproteins catalyse a diversity of fundamental redox reactions and are one of the most studied enzyme families. As monooxygenases, they are universally thought to control oxygenation by means of a peroxyflavin species that transfers a single atom ...

    Flavoproteins catalyse a diversity of fundamental redox reactions and are one of the most studied enzyme families. As monooxygenases, they are universally thought to control oxygenation by means of a peroxyflavin species that transfers a single atom of molecular oxygen to an organic substrate. Here we report that the bacterial flavoenzyme EncM catalyses the peroxyflavin-independent oxygenation-dehydrogenation dual oxidation of a highly reactive poly(β-carbonyl). The crystal structure of EncM with bound substrate mimics and isotope labelling studies reveal previously unknown flavin redox biochemistry. We show that EncM maintains an unexpected stable flavin-oxygenating species, proposed to be a flavin-N5-oxide, to promote substrate oxidation and trigger a rare Favorskii-type rearrangement that is central to the biosynthesis of the antibiotic enterocin. This work provides new insight into the fine-tuning of the flavin cofactor in offsetting the innate reactivity of a polyketide substrate to direct its efficient electrocyclization.


    Related Citations: 
    • Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement
      Teufel, R.,Miyanaga, A.,Michaudel, Q.,Stull, F.,Louie, G.,Noel, J.P.,Baran, P.S.,Palfey, B.,Moore, B.S.
      (2013) Nature 503: 552


    Organizational Affiliation

    Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAD-dependent oxygenase EncM
A, B, C, D
464Streptomyces maritimusMutation(s): 0 
Gene Names: encM
Find proteins for Q9KHK2 (Streptomyces maritimus)
Go to UniProtKB:  Q9KHK2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 166.060α = 90.00
b = 175.020β = 90.00
c = 132.290γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-01-13 
  • Released Date: 2015-01-28 
  • Deposition Author(s): Teufel, R.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI47818

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.2: 2017-11-22
    Type: Refinement description