4HHS

Crystal Structure of fatty acid alpha-dioxygenase (Arabidopsis thaliana)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of alpha-Dioxygenase provides insight into diversity in the cyclooxygenase-peroxidase superfamily.

Goulah, C.C.Zhu, G.Koszelak-Rosenblum, M.Malkowski, M.G.

(2013) Biochemistry 52: 1364-1372

  • DOI: 10.1021/bi400013k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • α-Dioxygenases (α-DOX) oxygenate fatty acids into 2(R)-hydroperoxides. Despite the low level of sequence identity, α-DOX share common catalytic features with cyclooxygenases (COX), including the use of a tyrosyl radical during catalysis. We determine ...

    α-Dioxygenases (α-DOX) oxygenate fatty acids into 2(R)-hydroperoxides. Despite the low level of sequence identity, α-DOX share common catalytic features with cyclooxygenases (COX), including the use of a tyrosyl radical during catalysis. We determined the X-ray crystal structure of Arabidopsis thaliana α-DOX to 1.5 Å resolution. The α-DOX structure is monomeric, predominantly α-helical, and comprised of two domains. The base domain exhibits a low degree of structural homology with the membrane-binding domain of COX but lies in a similar position with respect to the catalytic domain. The catalytic domain shows the highest degree of similarity with the COX catalytic domain, where 21 of the 22 α-helical elements are conserved. Helices H2, H6, H8, and H17 form the heme binding cleft and walls of the active site channel. His-318, Thr-323, and Arg-566 are located near the catalytic tyrosine, Tyr-386, at the apex of the channel, where they interact with a chloride ion. Substitutions at these positions coupled with kinetic analyses confirm previous hypotheses that implicate these residues as being involved in binding and orienting the carboxylate group of the fatty acid for optimal catalysis. Unique to α-DOX is the presence of two extended inserts on the surface of the enzyme that restrict access to the distal face of the heme, providing an explanation for the observed reduced peroxidase activity of the enzyme. The α-DOX structure represents the first member of the α-DOX subfamily to be structurally characterized within the cyclooxygenase-peroxidase family of heme-containing proteins.


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute, The State University of New York at Buffalo, New York 14203, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-dioxygenase
A
652Arabidopsis thalianaMutation(s): 0 
Gene Names: DOX1 (DIOX1, PADOX-1, PIOX)
EC: 1.14.99.-
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Cyclooxygenases
Protein: 
Fatty acid α-dioxygenase (α-DOX)
Find proteins for Q9SGH6 (Arabidopsis thaliana)
Go to UniProtKB:  Q9SGH6
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

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A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PGE
Query on PGE

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A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
BNG
Query on BNG

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A
B-NONYLGLUCOSIDE
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.159 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.150α = 90.00
b = 102.150β = 90.00
c = 137.565γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references