3DSK

Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase variant (F137L) (At-AOS(F137L), Cytochrome P450 74A, CYP74A) Complexed with 12R,13S-Vernolic Acid at 1.55 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural insights into the evolutionary paths of oxylipin biosynthetic enzymes

Lee, D.S.Nioche, P.Hamberg, M.Raman, C.S.

(2008) Nature 455: 363-368

  • DOI: https://doi.org/10.1038/nature07307
  • Primary Citation of Related Structures:  
    2RCH, 2RCL, 2RCM, 3CLI, 3DSI, 3DSJ, 3DSK

  • PubMed Abstract: 

    The oxylipin pathway generates not only prostaglandin-like jasmonates but also green leaf volatiles (GLVs), which confer characteristic aromas to fruits and vegetables. Although allene oxide synthase (AOS) and hydroperoxide lyase are atypical cytochrome P450 family members involved in the synthesis of jasmonates and GLVs, respectively, it is unknown how these enzymes rearrange their hydroperoxide substrates into different products. Here we present the crystal structures of Arabidopsis thaliana AOS, free and in complex with substrate or intermediate analogues. The structures reveal an unusual active site poised to control the reactivity of an epoxyallylic radical and its cation by means of interactions with an aromatic pi-system. Replacing the amino acid involved in these steps by a non-polar residue markedly reduces AOS activity and, unexpectedly, is both necessary and sufficient for converting AOS into a GLV biosynthetic enzyme. Furthermore, by combining our structural data with bioinformatic and biochemical analyses, we have discovered previously unknown hydroperoxide lyase in plant growth-promoting rhizobacteria, AOS in coral, and epoxyalcohol synthase in amphioxus. These results indicate that oxylipin biosynthetic genes were present in the last common ancestor of plants and animals, but were subsequently lost in all metazoan lineages except Placozoa, Cnidaria and Cephalochordata.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 74A, chloroplast
A, B
495Arabidopsis thalianaMutation(s): 1 
Gene Names: CYP74AAOSAt5g42650MJB21.2
EC: 4.2.1.92
Membrane Entity: Yes 
UniProt
Find proteins for Q96242 (Arabidopsis thaliana)
Explore Q96242 
Go to UniProtKB:  Q96242
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96242
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
T25
Query on T25

Download Ideal Coordinates CCD File 
D [auth A](9Z)-11-[(2R,3S)-3-pentyloxiran-2-yl]undec-9-enoic acid
C18 H32 O3
CCPPLLJZDQAOHD-BEBBCNLGSA-N
OCT
Query on OCT

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.612α = 90
b = 105.463β = 90
c = 162.632γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description