2WJ3

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural Basis for Cofactor-Independent Dioxygenation of N-Heteroaromatic Compounds at the {Alpha}/{Beta}-Hydrolase Fold.

Steiner, R.A., Janssen, H.J., Roversi, P., Oakley, A.J., Fetzner, S.

(2010) Proc.Natl.Acad.Sci.USA 107: 657

  • DOI: 10.1073/pnas.0909033107
  • Primary Citation of Related Structures:  
  • Also Cited By: 4CFS

  • PubMed Abstract: 

    • Enzymatic catalysis of oxygenation reactions in the absence of metal or organic cofactors is a considerable biochemical challenge. The CO-forming 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (HOD) from Arthrobacter nitroguajacolicus Rü61a and 1-H-3- ...

    Enzymatic catalysis of oxygenation reactions in the absence of metal or organic cofactors is a considerable biochemical challenge. The CO-forming 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (HOD) from Arthrobacter nitroguajacolicus Rü61a and 1-H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase (QDO) from Pseudomonas putida 33/1 are homologous cofactor-independent dioxygenases involved in the breakdown of N-heteroaromatic compounds. To date, they are the only dioxygenases suggested to belong to the alpha/beta-hydrolase fold superfamily. Members of this family typically catalyze hydrolytic processes rather than oxygenation reactions. We present here the crystal structures of both HOD and QDO in their native state as well as the structure of HOD in complex with its natural 1-H-3-hydroxy-4-oxoquinaldine substrate, its N-acetylanthranilate reaction product, and chloride as dioxygen mimic. HOD and QDO are structurally very similar. They possess a classical alpha/beta-hydrolase fold core domain additionally equipped with a cap domain. Organic substrates bind in a preorganized active site with an orientation ideally suited for selective deprotonation of their hydroxyl group by a His/Asp charge-relay system affording the generation of electron-donating species. The "oxyanion hole" of the alpha/beta-hydrolase fold, typically employed to stabilize the tetrahedral intermediate in ester hydrolysis reactions, is utilized here to host and control oxygen chemistry, which is proposed to involve a peroxide anion intermediate. Product release by proton back transfer from the catalytic histidine is driven by minimization of intramolecular charge repulsion. Structural and kinetic data suggest a nonnucleophilic general-base mechanism. Our analysis provides a framework to explain cofactor-independent dioxygenation within a protein architecture generally employed to catalyze hydrolytic reactions.

    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of 1H-3-Hydroxy-4-Oxoquinaldine 2,4-Dioxygenase from Arthrobacter Nitroguajacolicus Ru61A: A Cofactor-Devoid Dioxygenase of the Alpha/Beta-Hydrolase-Fold Superfamily.
      Steiner, R.A.,Frerichs-Deeken, U.,Fetzner, S.
      (2007) Acta Crystallogr.,Sect.F 63: 382

    Organizational Affiliation: 

    Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, England. roberto.steiner@kcl.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-H-3-HYDROXY-4-OXOQUINALDINE 2,4-DIOXYGENASE
A, B, C, D
276Paenarthrobacter nitroguajacolicusMutation(s): 1 
Gene Names: hod (meqE)
EC: 1.13.11.48
Find proteins for O31266 (Paenarthrobacter nitroguajacolicus)
Go to UniProtKB:  O31266
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SRT
Query on SRT
Download SDF File 
Download CCD File 
A, B, C, D
S,R MESO-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-XIXRPRMCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.170α = 90.00
b = 167.860β = 90.00
c = 168.030γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-05-20 
  • Released Date: 2010-01-26 
  • Deposition Author(s): Steiner, R.A.

Revision History 

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance