4XLO | pdb_00004xlo

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 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/10.1038/nature12643
  • Primary Citation Related Structures: 
    3W8W, 3W8X, 3W8Z, 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 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.


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

Macromolecule Content 

  • Total Structure Weight: 203.44 kDa 
  • Atom Count: 16,464 
  • Modeled Residue Count: 1,841 
  • Deposited Residue Count: 1,856 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FAD-dependent oxygenase EncM
A, B, C, D
464Streptomyces maritimusMutation(s): 0 
Gene Names: encM
UniProt
Find proteins for Q9KHK2 (Streptomyces maritimus)
Explore Q9KHK2 
Go to UniProtKB:  Q9KHK2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KHK2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free:  0.230 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.06α = 90
b = 175.02β = 90
c = 132.29γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI47818

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary