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Isomerase PDB id
2gin
Jmol
Contents
Protein chains
(+ 0 more) 173 a.a. *
Ligands
GOL ×5
Metals
_NA ×2
Waters ×660
* Residue conservation analysis
PDB id:
2gin
Name: Isomerase
Title: X-ray structure of the wt allene oxide cyclase 2 from arabid thaliana
Structure: Allene oxide cyclase 2. Chain: a, b, c, d, e, f. Fragment: allene oxide cyclase 2. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: at3g25770. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
1.80Å     R-factor:   0.207     R-free:   0.248
Authors: E.Hofmann,F.Schaller,P.Zerbe
Key ref: E.Hofmann et al. (2006). The crystal structure of Arabidopsis thaliana allene oxide cyclase: insights into the oxylipin cyclization reaction. Plant Cell, 18, 3201-3217. PubMed id: 17085685 DOI: 10.1105/tpc.106.043984
Date:
29-Mar-06     Release date:   21-Nov-06    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9LS02  (AOC2_ARATH) -  Allene oxide cyclase 2, chloroplastic
Seq:
Struc: 		253 a.a.
173 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.5.3.99.6  - Allene-oxide cyclase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (9Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate = (15Z)-12-oxophyto- 10,15-dienoate
(9Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate
 = (15Z)-12-oxophyto- 10,15-dienoate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     chloroplast   1 term 
  Biochemical function     isomerase activity     1 term  

 

 
    Added reference    
 
 
DOI no: 10.1105/tpc.106.043984 Plant Cell 18:3201-3217 (2006)
PubMed id: 17085685  
 
 
The crystal structure of Arabidopsis thaliana allene oxide cyclase: insights into the oxylipin cyclization reaction.
E.Hofmann, P.Zerbe, F.Schaller.
 
  ABSTRACT  
 
We describe the crystallization and structure elucidation of Arabidopsis thaliana allene oxide cyclase 2 (AOC2), a key enzyme in the biosynthesis of jasmonates. In a coupled reaction with allene oxide synthase, AOC2 releases the first cyclic and biologically active metabolite, 12-oxo-phytodienoic acid (OPDA). AOC2 (AT3G25770) folds into an eight-stranded antiparallel beta-barrel with a C-terminal partial helical extension. The protein forms a hydrophobic binding cavity with two distinct polar patches. AOC2 is trimeric in crystals, in vitro and in planta. Based on the observed folding pattern, we assigned AOC2 as a low molecular weight member of the lipocalin family with enzymatic activity in plants. We determined the binding position of the competitive inhibitor vernolic acid (a substrate analog) in the binding pocket. Based on models for bound substrate 12,13-epoxy-9,11,15-octadecatrienoic acid and product OPDA, we propose a reaction scheme that explains the influence of the C15 double bond on reactivity. Reaction is promoted by anchimeric assistance through a conserved Glu residue. The transition state with a pentadienyl carbocation and an oxyanion is stabilized by a strongly bound water molecule and favorable pi-pi interactions with aromatic residues in the cavity. Stereoselectivity results from steric restrictions to the necessary substrate isomerizations imposed by the protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20037473 G.Bonaventure, and I.T.Baldwin (2010).
New insights into the early biochemical activation of jasmonic acid biosynthesis in leaves.
  Plant Signal Behav, 5, 287-289.  
21106005 M.Luo, J.Liu, R.D.Lee, B.T.Scully, and B.Guo (2010).
Monitoring the expression of maize genes in developing kernels under drought stress using oligo-microarray.
  J Integr Plant Biol, 52, 1059-1074.  
18780387 A.N.Grechkin, L.S.Mukhtarova, L.R.Latypova, Y.Gogolev, Y.Y.Toporkova, and M.Hamberg (2008).
Tomato CYP74C3 is a multifunctional enzyme not only synthesizing allene oxide but also catalyzing its hydrolysis and cyclization.
  Chembiochem, 9, 2498-2505.  
18780388 C.Wasternack, and I.Feussner (2008).
Multifunctional enzymes in oxylipin metabolism.
  Chembiochem, 9, 2373-2375.  
18716621 D.S.Lee, P.Nioche, M.Hamberg, and C.S.Raman (2008).
Structural insights into the evolutionary paths of oxylipin biosynthetic enzymes.
  Nature, 455, 363-368.
PDB codes: 2rch 2rcl 2rcm 3cli 3dsi 3dsj 3dsk
18393998 F.Schaller, P.Zerbe, S.Reinbothe, C.Reinbothe, E.Hofmann, and S.Pollmann (2008).
The allene oxide cyclase family of Arabidopsis thaliana: localization and cyclization.
  FEBS J, 275, 2428-2441.  
18787124 L.Li, Z.Chang, Z.Pan, Z.Q.Fu, and X.Wang (2008).
Modes of heme binding and substrate access for cytochrome P450 CYP74A revealed by crystal structures of allene oxide synthase.
  Proc Natl Acad Sci U S A, 105, 13883-13888.
PDB codes: 3dam 3dan 3dbm
  18607105 Z.Chang, L.Li, Z.Pan, and X.Wang (2008).
Crystallization and preliminary X-ray analysis of allene oxide synthase, cytochrome P450 CYP74A2, from Parthenium argentatum.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 668-670.  
17957816 A.N.Grechkin, A.V.Ogorodnikova, O.I.Gnezdilov, and L.S.Mukhtarova (2007).
Detection of a pathway from linoleate to a novel cyclopentenone: cis-12-oxo-10-phytoenoic acid in sunflower roots.
  Chembiochem, 8, 2275-2280.  
17513307 C.Wasternack (2007).
Jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development.
  Ann Bot (Lond), 100, 681-697.  
17898899 P.H.Buist (2007).
Exotic biomodification of fatty acids.
  Nat Prod Rep, 24, 1110-1127.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.