2IX4

Arabidopsis thaliana mitochondrial beta-ketoacyl ACP synthase hexanoic acid complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the Human Beta-Ketoacyl [Acp] Synthase from the Mitochondrial Type II Fatty Acid Synthase.

Christensen, C.E.Kragelund, B.B.von Wettstein-Knowles, P.Henriksen, A.

(2007) Protein Sci 16: 261-272

  • DOI: 10.1110/ps.062473707
  • Primary Citation of Related Structures:  
    2IWY, 2IWZ, 2IX4

  • PubMed Abstract: 
  • Two distinct ways of organizing fatty acid biosynthesis exist: the multifunctional type I fatty acid synthase (FAS) of mammals, fungi, and lower eukaryotes with activities residing on one or two polypeptides; and the dissociated type II FAS of prokaryotes, plastids, and mitochondria with individual activities encoded by discrete genes ...

    Two distinct ways of organizing fatty acid biosynthesis exist: the multifunctional type I fatty acid synthase (FAS) of mammals, fungi, and lower eukaryotes with activities residing on one or two polypeptides; and the dissociated type II FAS of prokaryotes, plastids, and mitochondria with individual activities encoded by discrete genes. The beta-ketoacyl [ACP] synthase (KAS) moiety of the mitochondrial FAS (mtKAS) is targeted by the antibiotic cerulenin and possibly by the other antibiotics inhibiting prokaryotic KASes: thiolactomycin, platensimycin, and the alpha-methylene butyrolactone, C75. The high degree of structural similarity between mitochondrial and prokaryotic KASes complicates development of novel antibiotics targeting prokaryotic KAS without affecting KAS domains of cytoplasmic FAS. KASes catalyze the C(2) fatty acid elongation reaction using either a Cys-His-His or Cys-His-Asn catalytic triad. Three KASes with different substrate specificities participate in synthesis of the C(16) and C(18) products of prokaryotic FAS. By comparison, mtKAS carries out all elongation reactions in the mitochondria. We present the X-ray crystal structures of the Cys-His-His-containing human mtKAS and its hexanoyl complex plus the hexanoyl complex of the plant mtKAS from Arabidopsis thaliana. The structures explain (1) the bimodal (C(6) and C(10)-C(12)) substrate preferences leading to the C(8) lipoic acid precursor and long chains for the membranes, respectively, and (2) the low cerulenin sensitivity of the human enzyme; and (3) reveal two different potential acyl-binding-pocket extensions. Rearrangements taking place in the active site, including subtle changes in the water network, indicate a change in cooperativity of the active-site histidines upon primer binding.


    Related Citations: 
    • Structure of Mitochondrial Beta-Ketoacyl-(Acyl Carrier Protein) Synthase from Arabidopsis and its Role in Fatty Acid Synthesis
      Olsen, J.G., Rasmussen, A.V., von Wettstein-Knowles, P., Henriksen, A.
      (2004) FEBS Lett 577: 170

    Organizational Affiliation

    Department of Molecular Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASEA, B431Arabidopsis thalianaMutation(s): 0 
Gene Names: KASAt2g04540T1O3.5
EC: 2.3.1.41
UniProt
Find proteins for Q8L3X9 (Arabidopsis thaliana)
Explore Q8L3X9 
Go to UniProtKB:  Q8L3X9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8L3X9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6NA
Query on 6NA

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
HEXANOIC ACID
C6 H12 O2
FUZZWVXGSFPDMH-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.109α = 90
b = 92.942β = 106.59
c = 74.217γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-17
    Changes: Database references, Structure summary
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations