6SGL

Crystal structure of monooxygenase RutA complexed with Uracil under atmospheric pressure.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 

wwPDB Validation   3D Report Full Report


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:  
    6TEG, 6TEF, 6TEE, 6SGG, 6SGM, 6SGL, 6SGN

  • 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-(hy ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyrimidine monooxygenase RutAAAA364Escherichia coli K-12Mutation(s): 0 
Gene Names: rutAycdMb1012JW0997
EC: 1.14.99.46
Find proteins for P75898 (Escherichia coli (strain K12))
Explore P75898 
Go to UniProtKB:  P75898
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
AAA
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
URA
Query on URA

Download CCD File 
AAA
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
AAA
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.914α = 90
b = 87.914β = 90
c = 97.01γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History 

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