4DOY

Crystal structure of Dibenzothiophene desulfurization enzyme C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.789 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of DszC from Rhodococcus sp. XP at 1.79 angstrom

Liu, S.Zhang, C.Su, T.Wei, T.Zhu, D.Wang, K.Huang, Y.Dong, Y.Yin, K.Xu, S.Xu, P.Gu, L.

(2014) Proteins 82: 1708-1720

  • DOI: 10.1002/prot.24525

  • PubMed Abstract: 
  • The dibenzothiophene (DBT) monooxygenase DszC, which is the key initiating enzyme in "4S" metabolic pathway, catalyzes sequential sulphoxidation reaction of DBT to DBT sulfoxide (DBTO), then DBT sulfone (DBTO2). Here, we report the crystal structure ...

    The dibenzothiophene (DBT) monooxygenase DszC, which is the key initiating enzyme in "4S" metabolic pathway, catalyzes sequential sulphoxidation reaction of DBT to DBT sulfoxide (DBTO), then DBT sulfone (DBTO2). Here, we report the crystal structure of DszC from Rhodococcus sp. XP at 1.79 Å. Intriguingly, two distinct conformations occur in the flexible lid loops adjacent to the active site (residue 280-295, between α9 and α10). They are named "open"' and "closed" state respectively, and might show the status of the free and ligand-bound DszC. The molecular docking results suggest that the reduced FMN reacts with an oxygen molecule at C4a position of the isoalloxazine ring, producing the C4a-(hydro)peroxyflavin intermediate which is stabilized by H391 and S163. H391 may contribute to the formation of the C4a-(hydro)peroxyflavin by acting as a proton donor to the proximal peroxy oxygen, and it might also be involved in the protonation process of the C4a-(hydro)xyflavin. Site-directed mutagenesis study shows that mutations in the residues involved either in catalysis or in flavin or substrate-binding result in a complete loss of enzyme activity, suggesting that the accurate positions of flavin and substrate are crucial for the enzyme activity.


    Organizational Affiliation

    State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dibenzothiophene desulfurization enzyme C
A, B, C, D, E, F, G, H
437Rhodococcus sp. XPGene Names: dszC
Find proteins for Q6WNP1 (Rhodococcus sp. XP)
Go to UniProtKB:  Q6WNP1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.789 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 95.519α = 98.46
b = 98.824β = 106.99
c = 111.465γ = 107.07
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references
  • Version 1.2: 2014-12-24
    Type: Database references