3STU

Crystal Structure of tomato Methylketone Synthase I complexed with methyl-3-hydroxydodecanoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Emergent Decarboxylase Activity and Attenuation of alpha/beta-Hydrolase Activity during the Evolution of Methylketone Biosynthesis in Tomato.

Auldridge, M.E.Guo, Y.Austin, M.B.Ramsey, J.Fridman, E.Pichersky, E.Noel, J.P.

(2012) Plant Cell 24: 1596-1607

  • DOI: 10.1105/tpc.111.093997
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Specialized methylketone-containing metabolites accumulate in certain plants, in particular wild tomatoes in which they serve as toxic compounds against chewing insects. In Solanum habrochaites f. glabratum, methylketone biosynthesis occurs in the pl ...

    Specialized methylketone-containing metabolites accumulate in certain plants, in particular wild tomatoes in which they serve as toxic compounds against chewing insects. In Solanum habrochaites f. glabratum, methylketone biosynthesis occurs in the plastids of glandular trichomes and begins with intermediates of de novo fatty acid synthesis. These fatty-acyl intermediates are converted via sequential reactions catalyzed by Methylketone Synthase2 (MKS2) and MKS1 to produce the n-1 methylketone. We report crystal structures of S. habrochaites MKS1, an atypical member of the α/β-hydrolase superfamily. Sequence comparisons revealed the MKS1 catalytic triad, Ala-His-Asn, as divergent to the traditional α/β-hydrolase triad, Ser-His-Asp. Determination of the MKS1 structure points to a novel enzymatic mechanism dependent upon residues Thr-18 and His-243, confirmed by biochemical assays. Structural analysis further reveals a tunnel leading from the active site consisting mostly of hydrophobic residues, an environment well suited for fatty-acyl chain binding. We confirmed the importance of this substrate binding mode by substituting several amino acids leading to an alteration in the acyl-chain length preference of MKS1. Furthermore, we employ structure-guided mutagenesis and functional assays to demonstrate that MKS1, unlike enzymes from this hydrolase superfamily, is not an efficient hydrolase but instead catalyzes the decarboxylation of 3-keto acids.


    Organizational Affiliation

    Howard Hughes Medical Institute, The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA. auldridge@wisc.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methylketone synthase 1
A, B
267Lycopersicon hirsutum f. glabratumMutation(s): 0 
Gene Names: MKS1
Find proteins for E0YCS2 (Lycopersicon hirsutum f. glabratum)
Go to Gene View: MKS1
Go to UniProtKB:  E0YCS2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DK3
Query on DK3

Download SDF File 
Download CCD File 
B
methyl (3S)-3-hydroxydodecanoate
C13 H26 O3
OZXCINYANGIBDB-LBPRGKRZSA-N
 Ligand Interaction
DKA
Query on DKA

Download SDF File 
Download CCD File 
A
DECANOIC ACID
C10 H20 O2
GHVNFZFCNZKVNT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.197α = 90.00
b = 105.716β = 96.51
c = 59.888γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
SCALEPACKdata scaling
Blu-Icedata collection
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description