4H6B

Structural basis for allene oxide cyclization in moss


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of Physcomitrella patens AOC1 and AOC2: Insights into the Enzyme Mechanism and Differences in Substrate Specificity.

Neumann, P.Brodhun, F.Sauer, K.Herrfurth, C.Hamberg, M.Brinkmann, J.Scholz, J.Dickmanns, A.Feussner, I.Ficner, R.

(2012) Plant Physiol 160: 1251-1266

  • DOI: 10.1104/pp.112.205138
  • Primary Citation of Related Structures:  
    4H69, 4H6A, 4H6B, 4H6C

  • PubMed Abstract: 
  • In plants, oxylipins regulate developmental processes and defense responses. The first specific step in the biosynthesis of the cyclopentanone class of oxylipins is catalyzed by allene oxide cyclase (AOC) that forms cis(+)-12-oxo-phytodienoic acid. The moss Physcomitrella patens has two AOCs (PpAOC1 and PpAOC2) with different substrate specificities for C₁₈- and C₂₀-derived substrates, respectively ...

    In plants, oxylipins regulate developmental processes and defense responses. The first specific step in the biosynthesis of the cyclopentanone class of oxylipins is catalyzed by allene oxide cyclase (AOC) that forms cis(+)-12-oxo-phytodienoic acid. The moss Physcomitrella patens has two AOCs (PpAOC1 and PpAOC2) with different substrate specificities for C₁₈- and C₂₀-derived substrates, respectively. To better understand AOC's catalytic mechanism and to elucidate the structural properties that explain the differences in substrate specificity, we solved and analyzed the crystal structures of 36 monomers of both apo and ligand complexes of PpAOC1 and PpAOC2. From these data, we propose the following intermediates in AOC catalysis: (1) a resting state of the apo enzyme with a closed conformation, (2) a first shallow binding mode, followed by (3) a tight binding of the substrate accompanied by conformational changes in the binding pocket, and (4) initiation of the catalytic cycle by opening of the epoxide ring. As expected, the substrate dihydro analog cis-12,13S-epoxy-9Z,15Z-octadecadienoic acid did not cyclize in the presence of PpAOC1; however, when bound to the enzyme, it underwent isomerization into the corresponding trans-epoxide. By comparing complex structures of the C₁₈ substrate analog with in silico modeling of the C₂₀ substrate analog bound to the enzyme allowed us to identify three major molecular determinants responsible for the different substrate specificities (i.e. larger active site diameter, an elongated cavity of PpAOC2, and two nonidentical residues at the entrance of the active site).


    Organizational Affiliation

    Department of Molecular Structural Biology, Institute of Microbiology and Genetics, University of Goettingen, 37077 Goettingen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Allene oxide cyclase195Physcomitrium patensMutation(s): 0 
Gene Names: aocaoc1PHYPA_006604PHYPADRAFT_226795
EC: 5.3.99.6
UniProt
Find proteins for Q8GS38 (Physcomitrium patens)
Explore Q8GS38 
Go to UniProtKB:  Q8GS38
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GS38
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
10Y
Query on 10Y

Download Ideal Coordinates CCD File 
JA [auth G],
N [auth A]
(9Z)-11-{(2R,3S)-3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}undec-9-enoic acid
C18 H30 O3
BKKGUKSHPCTUGE-ZQCGFPFMSA-N
 Ligand Interaction
10X
Query on 10X

Download Ideal Coordinates CCD File 
M [auth A],
SA [auth J],
V [auth B]
(9Z)-11-{(2S,3S)-3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}undec-9-enoic acid
C18 H30 O3
BKKGUKSHPCTUGE-WXDGQRKDSA-N
 Ligand Interaction
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
CA [auth F],
FA [auth F],
GA [auth F],
MA [auth H],
NA [auth I],
CA [auth F],
FA [auth F],
GA [auth F],
MA [auth H],
NA [auth I],
Q [auth D],
TA [auth K],
U [auth C],
Y [auth B],
Z [auth E]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
DA [auth F],
EA [auth F],
HA [auth G],
AA [auth E],
BA [auth E],
DA [auth F],
EA [auth F],
HA [auth G],
IA [auth G],
KA [auth H],
LA [auth H],
O [auth A],
OA [auth I],
P [auth A],
PA [auth I],
QA [auth J],
R [auth D],
RA [auth J],
S [auth D],
T [auth C],
UA [auth K],
VA [auth K],
W [auth B],
WA [auth L],
X [auth B],
XA [auth L]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.42α = 84.36
b = 67.513β = 79.15
c = 161.879γ = 62.13
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Database references
  • Version 1.2: 2019-09-04
    Changes: Data collection