plant enzyme

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


The Crystal Structure of a Plant 3-Ketoacyl-Coa Thiolase Reveals the Potential for Redox Control of Peroxisomal Fatty Acid Beta-Oxidation.

Sundaramoorthy, R.Micossi, E.Alphey, M.S.Germain, V.Bryce, J.H.Smith, S.M.Leonard, G.A.Hunter, W.N.

(2006) J Mol Biol 359: 347

  • DOI: https://doi.org/10.1016/j.jmb.2006.03.032
  • Primary Citation of Related Structures:  
    2C7Y, 2C7Z

  • PubMed Abstract: 

    Crystal structures of peroxisomal Arabidopsis thaliana 3-ketoacyl-CoA thiolase (AtKAT), an enzyme of fatty acid beta-oxidation, are reported. The subunit, a typical thiolase, is a combination of two similar alpha/beta domains capped with a loop domain. The comparison of AtKAT with the Saccharomyces cerevisiae homologue (ScKAT) structure reveals a different placement of subunits within the functional dimers and that a polypeptide segment forming an extended loop around the open catalytic pocket of ScKAT converts to alpha-helix in AtKAT, and occludes the active site. A disulfide is formed between Cys192, on this helix, and Cys138, a catalytic residue. Access to Cys138 is determined by the structure of this polypeptide segment. AtKAT represents an oxidized, previously unknown inactive form, whilst ScKAT is the reduced and active enzyme. A high level of sequence conservation is observed, including Cys192, in eukaryotic peroxisomal, but not mitochondrial or prokaryotic KAT sequences, for this labile loop/helix segment. This indicates that KAT activity in peroxisomes is influenced by a disulfide/dithiol change linking fatty acid beta-oxidation with redox regulation.

  • Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
404Arabidopsis thalianaMutation(s): 0 
Find proteins for Q56WD9 (Arabidopsis thaliana)
Explore Q56WD9 
Go to UniProtKB:  Q56WD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56WD9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.154α = 90
b = 94.461β = 90
c = 111.499γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description