2WG9

Structure of Oryza Sativa (Rice) PLA2, complex with octanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of a Class Xib Phospholipase A2 (Pla2): Rice (Oryza Sativa) Isoform-2 Pla2 and an Octanoate Complex.

Guy, J.E.Stahl, U.Lindqvist, Y.

(2009) J.Biol.Chem. 284: 19371

  • DOI: 10.1074/jbc.M109.008466
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phospholipase A(2) catalyzes the specific hydrolysis of the sn-2 acyl bond of various glycerophospholipids, producing fatty acids and lysophospholipids. Phospholipase A(2)s (PLA(2)s) constitute a large superfamily of enzymes whose products are import ...

    Phospholipase A(2) catalyzes the specific hydrolysis of the sn-2 acyl bond of various glycerophospholipids, producing fatty acids and lysophospholipids. Phospholipase A(2)s (PLA(2)s) constitute a large superfamily of enzymes whose products are important for a multitude of signal transduction processes, lipid mediator release, lipid metabolism, development, plant stress responses, and host defense. The crystal structure of rice (Oryza sativa) isoform 2 phospholipase A(2) has been determined to 2.0 A resolution using sulfur SAD phasing, and shows that the class XIb phospholipases have a unique structure compared with other secreted PLA(2)s. The N-terminal half of the chain contains mainly loop structure, including the conserved Ca(2+)-binding loop, but starts with a short 3(10)-helix and also includes two short anti-parallel beta-strands. The C-terminal half is folded into three anti-parallel alpha-helices, of which the two first are also present in other secreted PLA(2)s and contain the conserved catalytic histidine and calcium liganding aspartate residues. The structure is stabilized by six disulfide bonds. The water structure around the calcium ion binding site suggests the involvement of a second water molecule in the mechanism for hydrolysis, the water-assisted calcium-coordinate oxyanion mechanism. The octanoate molecule in the complex structure is bound in a hydrophobic pocket, which extends to the likely membrane interface and is proposed to model the binding of the product fatty acid. Due to the differences in structure, the suggested surface for binding to the membrane has a different morphology in the rice PLA(2) compared with other phospholipases.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm S-17177, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE PHOSPHOLIPASE A2
A, B
130Oryza sativa subsp. japonicaMutation(s): 0 
Gene Names: PLA2-II
EC: 3.1.1.4
Find proteins for Q9XG81 (Oryza sativa subsp. japonica)
Go to UniProtKB:  Q9XG81
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
OCA
Query on OCA

Download SDF File 
Download CCD File 
A, B
OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 109.159α = 90.00
b = 109.159β = 90.00
c = 41.394γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-03-06
    Type: Advisory, Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-08
    Type: Data collection, Experimental preparation