2DE3

Crystal structure of DSZB C27S mutant in complex with 2'-hydroxybiphenyl-2-sulfinic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure and desulfurization mechanism of 2'-hydroxybiphenyl-2-sulfinic acid desulfinase.

Lee, W.C.Ohshiro, T.Matsubara, T.Izumi, Y.Tanokura, M.

(2006) J.Biol.Chem. 281: 32534-32539

  • DOI: 10.1074/jbc.M602974200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The desulfurization of dibenzothiophene in Rhodococcus erythropolis is catalyzed by two monooxygenases, DszA and DszC, and a desulfinase, DszB. In the last step of this pathway, DszB hydrolyzes 2'-hydroxybiphenyl-2-sulfinic acid into 2-hydroxybipheny ...

    The desulfurization of dibenzothiophene in Rhodococcus erythropolis is catalyzed by two monooxygenases, DszA and DszC, and a desulfinase, DszB. In the last step of this pathway, DszB hydrolyzes 2'-hydroxybiphenyl-2-sulfinic acid into 2-hydroxybiphenyl and sulfite. We report on the crystal structures of DszB and an inactive mutant of DszB in complex with substrates at resolutions of 1.8A or better. The overall fold of DszB is similar to those of periplasmic substrate-binding proteins. In the substrate complexes, biphenyl rings of substrates are recognized by extensive hydrophobic interactions with the active site residues. Binding of substrates accompanies structural changes of the active site loops and recruits His(60) to the active site. The sulfinate group of bound substrates forms hydrogen bonds with side chains of Ser(27), His(60), and Arg(70), each of which is shown by site-directed mutagenesis to be essential for the activity. In our proposed reaction mechanism, Cys(27) functions as a nucleophile and seems to be activated by the sulfinate group of substrates, whereas His(60) and Arg(70) orient the syn orbital of sulfinate oxygen to the sulfhydryl hydrogen of Cys(27) and stabilize the negatively charged reaction intermediate. Cys, His, and Arg residues are conserved in putative proteins homologous to DszB, which are presumed to constitute a new family of desulfinases.


    Organizational Affiliation

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyoku, Tokyo 113-8657.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIBENZOTHIOPHENE DESULFURIZATION ENZYME B
A, B
365Rhodococcus sp. (strain IGTS8)Mutation(s): 1 
Gene Names: soxB (dszB)
EC: 3.13.1.3
Find proteins for P54997 (Rhodococcus sp. (strain IGTS8))
Go to UniProtKB:  P54997
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
OBP
Query on OBP

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Download CCD File 
A, B
2'-HYDROXY-1,1'-BIPHENYL-2-SULFINIC ACID
2'-HYDROXYBIPHENYL-2-SULFINIC ACID
C12 H10 O3 S
HPKSNFTYZHYEKV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 154.670α = 90.00
b = 46.190β = 115.81
c = 113.960γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
CCP4data scaling
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-01
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance