6SGG

Crystal structure of monooxygenase RutA complexed with dioxygen under 1.5 MPa / 15 bars of oxygen pressure.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.154 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases.

Matthews, A.Saleem-Batcha, R.Sanders, J.N.Stull, F.Houk, K.N.Teufel, R.

(2020) Nat Chem Biol 16: 556-563

  • DOI: 10.1038/s41589-020-0476-2
  • Primary Citation of Related Structures:  
    6SGG, 6SGL, 6SGM, 6SGN, 6TEE, 6TEF, 6TEG

  • PubMed Abstract: 
  • One of the hallmark reactions catalyzed by flavin-dependent enzymes is the incorporation of an oxygen atom derived from dioxygen into organic substrates. For many decades, these flavin monooxygenases were assumed to use exclusively the flavin-C4a-(hydro)peroxide as their oxygen-transferring intermediate ...

    One of the hallmark reactions catalyzed by flavin-dependent enzymes is the incorporation of an oxygen atom derived from dioxygen into organic substrates. For many decades, these flavin monooxygenases were assumed to use exclusively the flavin-C4a-(hydro)peroxide as their oxygen-transferring intermediate. We demonstrate that flavoenzymes may instead employ a flavin-N5-peroxide as a soft α-nucleophile for catalysis, which enables chemistry not accessible to canonical monooxygenases. This includes, for example, the redox-neutral cleavage of carbon-hetero bonds or the dehalogenation of inert environmental pollutants via atypical oxygenations. We furthermore identify a shared structural motif for dioxygen activation and N5-functionalization, suggesting a conserved pathway that may be operative in numerous characterized and uncharacterized flavoenzymes from diverse organisms. Our findings show that overlooked flavin-N5-oxygen adducts are more widespread and may facilitate versatile chemistry, thus upending the notion that flavin monooxygenases exclusively function as nature's equivalents to organic peroxides in synthetic chemistry.


    Organizational Affiliation

    Faculty of Biology, University of Freiburg, Freiburg, Germany. robin.teufel@zbsa.uni-freiburg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyrimidine monooxygenase RutAA [auth AAA]363Escherichia coli K-12Mutation(s): 0 
Gene Names: rutAycdMb1012JW0997
EC: 1.14.99.46
UniProt
Find proteins for P75898 (Escherichia coli (strain K12))
Explore P75898 
Go to UniProtKB:  P75898
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75898
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
D [auth AAA]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth AAA]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth AAA]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
OXY (Subject of Investigation/LOI)
Query on OXY

Download Ideal Coordinates CCD File 
E [auth AAA]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.154 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.727α = 90
b = 87.727β = 90
c = 96.396γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyTE 931/2-1
German Research FoundationGermany235777276/GRK1976

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references