6FOQ

The crystal structure of EncM complexed with dioxygen under 15 bar of oxygen pressure.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.386 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Enzymatic control of dioxygen binding and functionalization of the flavin cofactor.

Saleem-Batcha, R.Stull, F.Sanders, J.N.Moore, B.S.Palfey, B.A.Houk, K.N.Teufel, R.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 4909-4914

  • DOI: 10.1073/pnas.1801189115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The reactions of enzymes and cofactors with gaseous molecules such as dioxygen (O <sub>2 </sub>) are challenging to study and remain among the most contentious subjects in biochemistry. To date, it is largely enigmatic how enzymes control and fine-tu ...

    The reactions of enzymes and cofactors with gaseous molecules such as dioxygen (O 2 ) are challenging to study and remain among the most contentious subjects in biochemistry. To date, it is largely enigmatic how enzymes control and fine-tune their reactions with O 2 , as exemplified by the ubiquitous flavin-dependent enzymes that commonly facilitate redox chemistry such as the oxygenation of organic substrates. Here we employ O 2 -pressurized X-ray crystallography and quantum mechanical calculations to reveal how the precise positioning of O 2 within a flavoenzyme's active site enables the regiospecific formation of a covalent flavin-oxygen adduct and oxygenating species (i.e., the flavin-N5-oxide) by mimicking a critical transition state. This study unambiguously demonstrates how enzymes may control the O 2 functionalization of an organic cofactor as prerequisite for oxidative catalysis. Our work thus illustrates how O 2 reactivity can be harnessed in an enzymatic environment and provides crucial knowledge for future rational design of O 2 -reactive enzymes.


    Organizational Affiliation

    Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109.,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095; houk@chem.ucla.edu robin.teufel@zbsa.uni-freiburg.de.,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095.,Center for Biological Systems Analysis (ZBSA), University of Freiburg, 79104 Freiburg, Germany.,Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA 92093.,Center for Biological Systems Analysis (ZBSA), University of Freiburg, 79104 Freiburg, Germany; houk@chem.ucla.edu robin.teufel@zbsa.uni-freiburg.de.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, B, C, D
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
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: 1.386 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 163.824α = 90.00
b = 175.153β = 90.00
c = 131.916γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyTE 931/2-1

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references