3VSJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


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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.,Sect.D 69: 32-43

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

  • 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 extradio ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-amino-5-chlorophenol 1,6-dioxygenase alpha subunit
A, C
271Comamonas testosteroniGene Names: cnbCa (amnA)
Find proteins for Q6J1Z5 (Comamonas testosteroni)
Go to UniProtKB:  Q6J1Z5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
2-amino-5-chlorophenol 1,6-dioxygenase beta subunit
B, D
312Comamonas testosteroniGene Names: cnbCb (amnB)
EC: 1.13.11.74, 1.13.11.76
Find proteins for Q6J1Z6 (Comamonas testosteroni)
Go to UniProtKB:  Q6J1Z6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
OH
Query on OH

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Download CCD File 
D
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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B, D
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
2X7
Query on 2X7

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Download CCD File 
D
(3E)-3-iminooxepin-2(3H)-one
(4Z,6Z)-3-iminooxepin-2(3H)-one
C6 H5 N O2
HQPIXVSGYRVKOL-FNORWQNLSA-N
 Ligand Interaction
2XP
Query on 2XP

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Download CCD File 
B
(2Z,4Z)-2-imino-6-oxohex-4-enoic acid
C6 H7 N O3
IZBQCPKKCVTOTK-PQZOIKATSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 270.240α = 90.00
b = 48.390β = 109.57
c = 108.550γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CrystalCleardata collection
REFMACrefinement
PHASESphasing
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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