3WKU

Crystal structure of the anaerobic DesB-gallate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1371/journal.pone.0092249
  • Primary Citation of Related Structures:  

  • 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 ...

    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 Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan.,Department of Materials Chemistry, Asahikawa National College of Technology, Asahikawa, Hokkaido, Japan.,Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gallate dioxygenase
A, B
418Sphingobium sp. (strain NBRC 103272 / SYK-6)Mutation(s): 0 
Gene Names: desB
Find proteins for G2IKE5 (Sphingobium sp. (strain NBRC 103272 / SYK-6))
Go to UniProtKB:  G2IKE5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
GDE
Query on GDE

Download SDF File 
Download CCD File 
A
3,4,5-trihydroxybenzoic acid
Gallate
C7 H6 O5
LNTHITQWFMADLM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.435α = 90.00
b = 60.765β = 98.58
c = 117.986γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
ADSCdata collection
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Experimental preparation