3VSJ

Crystal structure of 1,6-APD (2-ANIMOPHENOL-1,6-DIOXYGENASE) complexed with intermediate products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor

Li, D.F.Zhang, J.Y.Hou, Y.J.Liu, L.Hu, Y.Liu, S.J.Wang, D.C.Liu, W.

(2013) Acta Crystallogr D Biol Crystallogr 69: 32-43

  • DOI: 10.1107/S0907444912042072
  • Primary Citation of Related Structures:  
    3VSG, 3VSH, 3VSI, 3VSJ

  • PubMed Abstract: 
  • Dioxygen activation by nonhaem Fe(II) enzymes containing the 2-His-1-carboxylate facial triad has been extensively studied in recent years. Here, crystal structures of 2-aminophenol 1,6-dioxygenase, an enzyme that represents a minor group of extradiol dioxygenases and that catalyses the ring opening of 2-aminophenol, in complex with the lactone intermediate (4Z,6Z)-3-iminooxepin-2(3H)-one and the product 2-aminomuconic 6-semialdehyde and in complex with the suicide inhibitor 4-nitrocatechol are reported ...

    Dioxygen activation by nonhaem Fe(II) enzymes containing the 2-His-1-carboxylate facial triad has been extensively studied in recent years. Here, crystal structures of 2-aminophenol 1,6-dioxygenase, an enzyme that represents a minor group of extradiol dioxygenases and that catalyses the ring opening of 2-aminophenol, in complex with the lactone intermediate (4Z,6Z)-3-iminooxepin-2(3H)-one and the product 2-aminomuconic 6-semialdehyde and in complex with the suicide inhibitor 4-nitrocatechol are reported. The Fe-ligand binding schemes observed in these structures revealed some common geometrical characteristics that are shared by the published structures of extradiol dioxygenases, suggesting that enzymes that catalyse the oxidation of noncatecholic compounds are very likely to utilize a similar strategy for dioxygen activation and the fission of aromatic rings as the canonical mechanism. The Fe-ligation arrangement, however, is strikingly enantiomeric to that of all other 2-His-1-carboxylate enzymes apart from protocatechuate 4,5-dioxygenase. This structural variance leads to the generation of an uncommon O(-)-Fe(2+)-O(-) species prior to O(2) binding, which probably forms the structural basis on which APD distinguishes its specific substrate and inhibitor, which share an analogous molecular structure.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-amino-5-chlorophenol 1,6-dioxygenase alpha subunitA, C271Comamonas testosteroni CNB-1Mutation(s): 0 
EC: 1.13.11.8
UniProt
Find proteins for Q6J1Z5 (Comamonas testosteroni)
Explore Q6J1Z5 
Go to UniProtKB:  Q6J1Z5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
2-amino-5-chlorophenol 1,6-dioxygenase beta subunitB, D312Comamonas testosteroni CNB-1Mutation(s): 0 
EC: 1.13.11.8 (PDB Primary Data), 1.13.11.74 (UniProt), 1.13.11.76 (UniProt)
UniProt
Find proteins for Q6J1Z6 (Comamonas testosteroni)
Explore Q6J1Z6 
Go to UniProtKB:  Q6J1Z6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2XP
Query on 2XP

Download Ideal Coordinates CCD File 
G [auth B](2Z,4Z)-2-imino-6-oxohex-4-enoic acid
C6 H7 N O3
IZBQCPKKCVTOTK-PQZOIKATSA-N
 Ligand Interaction
2X7
Query on 2X7

Download Ideal Coordinates CCD File 
I [auth D](3E)-3-iminooxepin-2(3H)-one
C6 H5 N O2
HQPIXVSGYRVKOL-FNORWQNLSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
F [auth B], H [auth D]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
OH
Query on OH

Download Ideal Coordinates CCD File 
J [auth D]HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 270.24α = 90
b = 48.39β = 109.57
c = 108.55γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release