5XKC

Crystal structure of dibenzothiophene sulfone monooxygenase BdsA at 2.2 angstrome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.209 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Biochemical Characterization of BdsA fromBacillus subtilisWU-S2B, a Key Enzyme in the "4S" Desulfurization Pathway.

Su, T.Su, J.Liu, S.Zhang, C.He, J.Huang, Y.Xu, S.Gu, L.

(2018) Front Microbiol 9: 231-231

  • DOI: 10.3389/fmicb.2018.00231
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dibenzothiophene (DBT) and their derivatives, accounting for the major part of the sulfur components in crude oil, make one of the most significant pollution sources. The DBT sulfone monooxygenase BdsA, one of the key enzymes in the "4S" desulfurizat ...

    Dibenzothiophene (DBT) and their derivatives, accounting for the major part of the sulfur components in crude oil, make one of the most significant pollution sources. The DBT sulfone monooxygenase BdsA, one of the key enzymes in the "4S" desulfurization pathway, catalyzes the oxidation of DBT sulfone to 2'-hydroxybiphenyl 2-sulfonic acid (HBPSi). Here, we determined the crystal structure of BdsA from Bacillus subtilis WU-S2B, at the resolution of 2.2 Å, and the structure of the BdsA-FMN complex at 2.4 Å. BdsA and the BdsA-FMN complex exist as tetramers. DBT sulfone was placed into the active site by molecular docking. Seven residues (Phe12, His20, Phe56, Phe246, Val248, His316, and Val372) are found to be involved in the binding of DBT sulfone. The importance of these residues is supported by the study of the catalytic activity of the active site variants. Structural analysis and enzyme activity assay confirmed the importance of the right position and orientation of FMN and DBT sulfone, as well as the involvement of Ser139 as a nucleophile in catalysis. This work combined with our previous structure of DszC provides a systematic structural basis for the development of engineered desulfurization enzymes with higher efficiency and stability.


    Organizational Affiliation

    Faculty of Light Industry, Province Key Laboratory of Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China.,State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dibenzothiophene desulfurization enzyme A
A, B, C, D
453Bacillus subtilisMutation(s): 0 
Gene Names: bdsA
Find proteins for Q8GRC7 (Bacillus subtilis)
Go to UniProtKB:  Q8GRC7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.209 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 132.494α = 90.00
b = 174.574β = 90.00
c = 85.345γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2019-11-20
    Type: Database references
  • Version 1.2: 2019-12-18
    Type: Database references