RCSB PDB - 3WKU: Crystal structure of the anaerobic DesB-gallate complex

 3WKU

Crystal structure of the anaerobic DesB-gallate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDEClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6

Sugimoto, K.Senda, M.Kasai, D.Fukuda, M.Masai, E.Senda, T.

(2014) PLoS One 9: e92249-e92249

  • DOI: https://doi.org/10.1371/journal.pone.0092249
  • Primary Citation of Related Structures:  
    3WKU, 3WPM, 3WR3, 3WR4, 3WR8, 3WR9, 3WRA, 3WRB, 3WRC

  • PubMed Abstract: 

    DesB, which is derived from Sphingobium sp. SYK-6, is a type II extradiol dioxygenase that catalyzes a ring opening reaction of gallate. While typical extradiol dioxygenases show broad substrate specificity, DesB has strict substrate specificity for gallate. The substrate specificity of DesB seems to be required for the efficient growth of S. sp. SYK-6 using lignin-derived aromatic compounds. Since direct coordination of hydroxyl groups of the substrate to the non-heme iron in the active site is a critical step for the catalytic reaction of the extradiol dioxygenases, the mechanism of the substrate recognition and coordination of DesB was analyzed by biochemical and crystallographic methods. Our study demonstrated that the direct coordination between the non-heme iron and hydroxyl groups of the substrate requires a large shift of the Fe (II) ion in the active site. Mutational analysis revealed that His124 and His192 in the active site are essential to the catalytic reaction of DesB. His124, which interacts with OH (4) of the bound gallate, seems to contribute to proper positioning of the substrate in the active site. His192, which is located close to OH (3) of the gallate, is likely to serve as the catalytic base. Glu377' interacts with OH (5) of the gallate and seems to play a critical role in the substrate specificity. Our biochemical and structural study showed the substrate recognition and catalytic mechanisms of DesB.


  • Organizational Affiliation

    Department of Materials Chemistry, Asahikawa National College of Technology, Asahikawa, Hokkaido, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gallate dioxygenase
A, B
418Sphingobium sp. SYK-6Mutation(s): 0 
Gene Names: desB
EC: 1.13.11.58
UniProt
Find proteins for G2IKE5 (Sphingobium sp. (strain NBRC 103272 / SYK-6))
Explore G2IKE5 
Go to UniProtKB:  G2IKE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2IKE5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.435α = 90
b = 60.765β = 98.58
c = 117.986γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDEClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Experimental preparation
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations