2WU9

Crystal structure of peroxisomal KAT2 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Peroxisomal Plant 3-Ketoacyl-Coa Thiolases Structure and Activity are Regulated by a Sensitive Redox Switch

Pye, V.E.Christensen, C.E.Dyer, J.H.Arent, S.Henriksen, A.

(2010) J.Biol.Chem. 285: 24078

  • DOI: 10.1074/jbc.M110.106013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The breakdown of fatty acids, performed by the beta-oxidation cycle, is crucial for plant germination and sustainability. beta-Oxidation involves four enzymatic reactions. The final step, in which a two-carbon unit is cleaved from the fatty acid, is ...

    The breakdown of fatty acids, performed by the beta-oxidation cycle, is crucial for plant germination and sustainability. beta-Oxidation involves four enzymatic reactions. The final step, in which a two-carbon unit is cleaved from the fatty acid, is performed by a 3-ketoacyl-CoA thiolase (KAT). The shortened fatty acid may then pass through the cycle again (until reaching acetoacetyl-CoA) or be directed to a different cellular function. Crystal structures of KAT from Arabidopsis thaliana and Helianthus annuus have been solved to 1.5 and 1.8 A resolution, respectively. Their dimeric structures are very similar and exhibit a typical thiolase-like fold; dimer formation and active site conformation appear in an open, active, reduced state. Using an interdisciplinary approach, we confirmed the potential of plant KATs to be regulated by the redox environment in the peroxisome within a physiological range. In addition, co-immunoprecipitation studies suggest an interaction between KAT and the multifunctional protein that is responsible for the preceding two steps in beta-oxidation, which would allow a route for substrate channeling. We suggest a model for this complex based on the bacterial system.


    Organizational Affiliation

    Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark. vpye@tcd.ie




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-KETOACYL-COA THIOLASE 2, PEROXISOMAL
A, B
442Arabidopsis thalianaMutation(s): 0 
Gene Names: PED1 (KAT2)
EC: 2.3.1.16
Find proteins for Q56WD9 (Arabidopsis thaliana)
Go to UniProtKB:  Q56WD9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.831α = 90.00
b = 86.670β = 106.71
c = 72.750γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-12
    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: 2019-05-08
    Type: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-07-24
    Type: Data collection