8T0U | pdb_00008t0u

Crystal structure of dimethylsulfone monooxygenase SfnG from Pseudomonas fluorescens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Structural, biophysical, and biochemical insights into C-S bond cleavage by dimethylsulfone monooxygenase.

Gonzalez, R.Soule, J.Phan, N.Wicht, D.K.Dowling, D.P.

(2024) Proc Natl Acad Sci U S A 121: e2401858121-e2401858121

  • DOI: https://doi.org/10.1073/pnas.2401858121
  • Primary Citation of Related Structures:  
    8T0U, 8T0W

  • PubMed Abstract: 

    Sulfur is an essential element for life. Bacteria can obtain sulfur from inorganic sulfate; but in the sulfur starvation-induced response, Pseudomonads employ two-component flavin-dependent monooxygenases (TC-FMOs) from the msu and sfn operons to assimilate sulfur from environmental compounds including alkanesulfonates and dialkylsulfones. Here, we report binding studies of oxidized FMN to enzymes involved within the P. fluorescens enzymatic pathway responsible for converting dimethylsulfone (DMSO 2 ) to sulfite. In this catabolic pathway, SfnG serves as the initial TC-FMO for sulfur assimilation, which is investigated in detail by solving the 2.6-Å resolution crystal structure of unliganded SfnG and the 1.75-Å resolution crystal structure of the SfnG ternary complex containing FMN and DMSO 2 . We find that SfnG adopts a (β/α) 8 barrel fold with a distinct quaternary configuration from other tetrameric class C TC-FMOs. To probe the unexpected tetramer arrangement, structural heterogeneity is assessed by chromatography and light scattering to confirm ligand binding correlates with a tetramer. Binding of FMN and DMSO 2 accompanies ordering of the active site, with DMSO 2 bound on the si -face of the flavin. A previously unobserved protein backbone conformation is found within the oxygen-binding site on the re -face of the flavin. Functional assays and the positioning of ligands with respect to the oxygen-binding site are consistent with use of an N5-(hydro)peroxyflavin pathway. Biochemical endpoint assays and docking studies reveal SfnG breaks the C-S bond of a range of dialkylsulfones.


  • Organizational Affiliation
    • Department of Chemistry, University of Massachusetts, Boston, MA 02125.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FMNH(2)-dependent dimethylsulfone monooxygenase
A, B, C, D, E
A, B, C, D, E, F, G, H
387Pseudomonas fluorescens Pf0-1Mutation(s): 0 
Gene Names: sfnGPfl01_2879
EC: 1.14.14.35
UniProt
Find proteins for Q3KC85 (Pseudomonas fluorescens (strain Pf0-1))
Explore Q3KC85 
Go to UniProtKB:  Q3KC85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3KC85
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth H]
BA [auth H]
I [auth A]
J [auth A]
K [auth B]
AA [auth H],
BA [auth H],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth D],
Q [auth D],
R [auth D],
S [auth E],
T [auth E],
U [auth F],
V [auth F],
W [auth F],
X [auth G],
Y [auth G],
Z [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.785α = 103.827
b = 94.506β = 100.585
c = 102.056γ = 96.521
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1807480

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release