6NEV

FAD-dependent monooxygenase TropB from T. stipitatus Y239F Variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.303 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for selectivity in flavin-dependent monooxygenase-catalyzed oxidative dearomatization.

Rodriguez Benitez, A.Tweedy, S.E.Baker Dockrey, S.A.Lukowski, A.L.Wymore, T.Khare, D.Brooks 3rd, C.L.Palfey, B.A.Smith, J.L.Narayan, A.R.H.

(2019) Acs Catalysis 9: 3633-3640

  • DOI: 10.1021/acscatal.8b04575
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Biocatalytic reactions embody many features of ideal chemical transformations, including the potential for impeccable selectivity, high catalytic efficiency, mild reaction conditions and the use of environmentally benign reagents. These advantages ha ...

    Biocatalytic reactions embody many features of ideal chemical transformations, including the potential for impeccable selectivity, high catalytic efficiency, mild reaction conditions and the use of environmentally benign reagents. These advantages have created a demand for biocatalysts that expand the portfolio of complexity-generating reactions available to synthetic chemists. However, the tradeoff that often exists between the substrate scope of a biocatalyst and its selectivity limits the application of enzymes in synthesis. We recently demonstrated that a flavin-dependent monooxygenase, TropB, maintains high levels of site- and stereoselectivity across a range of structurally diverse substrates. Herein, we disclose the structural basis for substrate binding in TropB, which performs a synthetically challenging asymmetric oxidative dearomatization reaction with exquisite site- and stereoselectivity across a range of phenol substrates, providing a foundation for future protein engineering and reaction development efforts. Our hypothesis for substrate binding is informed by a crystal structure of TropB and molecular dynamics simulations with the corresponding computational TropB model and is supported by experimental data. In contrast to canonical class A FAD-dependent monooxygenases in which substrates bind in a protonated form, our data indicate that the phenolate form of the substrate binds in the active site. Furthermore, the substrate position is controlled through twopoint binding of the phenolate oxygen to Arg206 and Tyr239, which are shown to have distinct and essential roles in catalysis. Arg206 is involved in the reduction of the flavin cofactor, suggesting a role in flavin dynamics. Further, QM/MM simulations reveal the interactions that govern the facial selectivity that leads to a highly enantioselective transformation. Thus, the structural origins of the high levels of site-and stereoselectivity observed in reactions of TropB across a range of substrates are elucidated, providing a foundation for future protein engineering and reaction development efforts.


    Organizational Affiliation

    Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor Michigan 48109.,Life Sciences Institute, University of Michigan, Ann Arbor Michigan, 48109.,Program in Chemical Biology, University of Michigan, Ann arbor Michigan 48109.,Department of Biophysics, University of Michigan, Ann Arbor Michigan, 48109.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAD-dependent monooxygenase tropB
A, B
447Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006)Mutation(s): 1 
Gene Names: tropB (tsL1)
EC: 1.-.-.-
Find proteins for B8M9J8 (Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006))
Go to UniProtKB:  B8M9J8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.303 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 70.259α = 90.00
b = 184.508β = 90.00
c = 163.257γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
XDSdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM124880
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK042303

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release