4HHR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

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Ligand Structure Quality Assessment 


This is version 1.2 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:  
    4HHR, 4HHS

  • 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 determined the X-ray crystal structure of Arabidopsis thaliana α-DOX to 1 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-dioxygenaseA652Arabidopsis thalianaMutation(s): 0 
Gene Names: T13O15.6alphaDOX1At3g01420/T13O15.6DOX1At3g01420DIOX1PADOX-1PIOX
EC: 1.14.99
UniProt
Find proteins for Q9SGH6 (Arabidopsis thaliana)
Explore Q9SGH6 
Go to UniProtKB:  Q9SGH6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SGH6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BNG
Query on BNG

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O [auth A]nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
P6G
Query on P6G

Download Ideal Coordinates CCD File 
P [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth A],
S [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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C [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
CA
Query on CA

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D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
N [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.935α = 90
b = 101.935β = 90
c = 137.51γ = 90
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
SHELXSphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary