4P9G

Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

Starting Models: experimental
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Literature

Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP

Keegan, R.Lebedev, A.Erskine, P.Guo, J.Wood, S.P.Hopper, D.J.Rigby, S.E.J.Cooper, J.B.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2444-2454

  • DOI: https://doi.org/10.1107/S1399004714015053
  • Primary Citation of Related Structures:  
    4P9G

  • PubMed Abstract: 

    The enzyme 2,4'-dihydroxyacetophenone dioxygenase (DAD) catalyses the conversion of 2,4'-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid with the incorporation of molecular oxygen. Whilst the vast majority of dioxygenases cleave within the aromatic ring of the substrate, DAD is very unusual in that it is involved in C-C bond cleavage in a substituent of the aromatic ring. There is evidence that the enzyme is a homotetramer of 20.3 kDa subunits, each containing nonhaem iron, and its sequence suggests that it belongs to the cupin family of dioxygenases. In this paper, the first X-ray structure of a DAD enzyme from the Gram-negative bacterium Alcaligenes sp. 4HAP is reported, at a resolution of 2.2 Å. The structure establishes that the enzyme adopts a cupin fold, forming dimers with a pronounced hydrophobic interface between the monomers. The catalytic iron is coordinated by three histidine residues (76, 78 and 114) within a buried active-site cavity. The iron also appears to be tightly coordinated by an additional ligand which was putatively assigned as a carbonate dianion since this fits the electron density optimally, although it might also be the product formate. The modelled carbonate is located in a position which is highly likely to be occupied by the α-hydroxyketone group of the bound substrate during catalysis. Modelling of a substrate molecule in this position indicates that it will interact with many conserved amino acids in the predominantly hydrophobic active-site pocket where it undergoes peroxide radical-mediated heterolysis.


  • Organizational Affiliation

    STFC Rutherford Appleton Laboratory, RAL, Harwell Oxford, Didcot OX11 0FA, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2,4'-dihydroxyacetophenone dioxygenase197Alcaligenes sp.Mutation(s): 0 
Gene Names: dad
EC: 1.13.11.41
UniProt
Find proteins for Q9REI7 (Alcaligenes sp)
Explore Q9REI7 
Go to UniProtKB:  Q9REI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9REI7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.557α = 90
b = 82.557β = 90
c = 114.008γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
BALBESphasing
MOLREPphasing
ARPmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description