3X0X

Crystal structure of apo-DszC from Rhodococcus erythropolis D-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of apo-DszC and FMN-bound DszC from Rhodococcus erythropolis D-1.

Guan, L.J.Lee, W.C.Wang, S.Ohshiro, T.Izumi, Y.Ohtsuka, J.Tanokura, M.

(2015) FEBS J 282: 3126-3135

  • DOI: https://doi.org/10.1111/febs.13216
  • Primary Citation of Related Structures:  
    3X0X, 3X0Y

  • PubMed Abstract: 

    The release of SO2 from petroleum products derived from crude oil, which contains sulfur compounds such as dibenzothiophene (DBT), leads to air pollution. The '4S' metabolic pathway catalyzes the sequential conversion of DBT to 2-hydroxybiphenyl via three enzymes encoded by the dsz operon in several bacterial species. DszC (DBT monooxygenase), from Rhodococcus erythropolis D-1 is involved in the first two steps of the '4S' pathway. Here, we determined the first crystal structure of FMN-bound DszC, and found that two distinct conformations occur in the loop region (residues 131-142) adjacent to the active site. On the basis of the DszC-FMN structure and the previously reported apo structures of DszC homologs, the binding site for DBT and DBT sulfoxide is proposed.


  • Organizational Affiliation

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DszC417Rhodococcus erythropolisMutation(s): 0 
Gene Names: dszC
UniProt
Find proteins for A0A0C6DRW4 (Rhodococcus erythropolis)
Explore A0A0C6DRW4 
Go to UniProtKB:  A0A0C6DRW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0C6DRW4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.13α = 90
b = 123.25β = 101.21
c = 184.27γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references