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 3DY5 | pdb_00003dy5

Allene oxide synthase 8R-lipoxygenase from Plexaura homomalla


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 
    0.322 (Depositor), 0.303 (DCC) 
  • R-Value Work: 
    0.273 (Depositor), 0.261 (DCC) 
  • R-Value Observed: 
    0.275 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

A covalent linker allows for membrane targeting of an oxylipin biosynthetic complex.

Gilbert, N.C., Niebuhr, M., Tsuruta, H., Bordelon, T., Ridderbusch, O., Dassey, A., Brash, A.R., Bartlett, S.G., Newcomer, M.E.

(2008) Biochemistry 47: 10665-10676

  • DOI: https://doi.org/10.1021/bi800751p
  • Primary Citation Related Structures: 
    3DY5

  • PubMed Abstract: 

    A naturally occurring bifunctional protein from Plexaura homomalla links sequential catalytic activities in an oxylipin biosynthetic pathway. The C-terminal lipoxygenase (LOX) portion of the molecule catalyzes the transformation of arachidonic acid (AA) to the corresponding 8 R-hydroperoxide, and the N-terminal allene oxide synthase (AOS) domain promotes the conversion of the hydroperoxide intermediate to the product allene oxide (AO). Small-angle X-ray scattering data indicate that in the absence of a covalent linkage the two catalytic domains that transform AA to AO associate to form a complex that recapitulates the structure of the bifunctional protein. The SAXS data also support a model for LOX and AOS domain orientation in the fusion protein inferred from a low-resolution crystal structure. However, results of membrane binding experiments indicate that covalent linkage of the domains is required for Ca (2+)-dependent membrane targeting of the sequential activities, despite the noncovalent domain association. Furthermore, membrane targeting is accompanied by a conformational change as monitored by specific proteolysis of the linker that joins the AOS and LOX domains. Our data are consistent with a model in which Ca (2+)-dependent membrane binding relieves the noncovalent interactions between the AOS and LOX domains and suggests that the C2-like domain of LOX mediates both protein-protein and protein-membrane interactions.


  • Organizational Affiliation: 
    • Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

Macromolecule Content 

  • Total Structure Weight: 245.28 kDa 
  • Atom Count: 16,218 
  • Modeled Residue Count: 2,004 
  • Deposited Residue Count: 2,132 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Allene oxide synthase-lipoxygenase proteinA,
B [auth C]
1,066Plexaura homomallaMutation(s): 0 
EC: 4.2.1.92 (PDB Primary Data), 1.13.11.40 (PDB Primary Data), 4.2.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for O16025 (Plexaura homomalla)
Explore O16025 
Go to UniProtKB:  O16025
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO16025
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free:  0.322 (Depositor), 0.303 (DCC) 
  • R-Value Work:  0.273 (Depositor), 0.261 (DCC) 
  • R-Value Observed: 0.275 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 235.52α = 90
b = 77.493β = 112.45
c = 157.966γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Derived calculations, Structure summary