1ZGA

Crystal structure of isoflavanone 4'-O-methyltransferase complexed with (+)-6a-hydroxymaackiain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for dual functionality of isoflavonoid O-methyltransferases in the evolution of plant defense responses.

Liu, C.J.Deavours, B.E.Richard, S.B.Ferrer, J.L.Blount, J.W.Huhman, D.Dixon, R.A.Noel, J.P.

(2006) Plant Cell 18: 3656-3669

  • DOI: 10.1105/tpc.106.041376
  • Primary Citation of Related Structures:  1ZG3, 1ZGJ, 1ZHF

  • PubMed Abstract: 
  • In leguminous plants such as pea (Pisum sativum), alfalfa (Medicago sativa), barrel medic (Medicago truncatula), and chickpea (Cicer arietinum), 4'-O-methylation of isoflavonoid natural products occurs early in the biosynthesis of defense chemicals k ...

    In leguminous plants such as pea (Pisum sativum), alfalfa (Medicago sativa), barrel medic (Medicago truncatula), and chickpea (Cicer arietinum), 4'-O-methylation of isoflavonoid natural products occurs early in the biosynthesis of defense chemicals known as phytoalexins. However, among these four species, only pea catalyzes 3-O-methylation that converts the pterocarpanoid isoflavonoid 6a-hydroxymaackiain to pisatin. In pea, pisatin is important for chemical resistance to the pathogenic fungus Nectria hematococca. While barrel medic does not biosynthesize 6a-hydroxymaackiain, when cell suspension cultures are fed 6a-hydroxymaackiain, they accumulate pisatin. In vitro, hydroxyisoflavanone 4'-O-methyltransferase (HI4'OMT) from barrel medic exhibits nearly identical steady state kinetic parameters for the 4'-O-methylation of the isoflavonoid intermediate 2,7,4'-trihydroxyisoflavanone and for the 3-O-methylation of the 6a-hydroxymaackiain isoflavonoid-derived pterocarpanoid intermediate found in pea. Protein x-ray crystal structures of HI4'OMT substrate complexes revealed identically bound conformations for the 2S,3R-stereoisomer of 2,7,4'-trihydroxyisoflavanone and the 6aR,11aR-stereoisomer of 6a-hydroxymaackiain. These results suggest how similar conformations intrinsic to seemingly distinct chemical substrates allowed leguminous plants to use homologous enzymes for two different biosynthetic reactions. The three-dimensional similarity of natural small molecules represents one explanation for how plants may rapidly recruit enzymes for new biosynthetic reactions in response to changing physiological and ecological pressures.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isoflavanone 4'-O-methyltransferase'
A
357Medicago truncatulaGene Names: HI4'OMT
EC: 2.1.1.46, 2.1.1.212
Find proteins for Q29U70 (Medicago truncatula)
Go to UniProtKB:  Q29U70
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
HMK
Query on HMK

Download SDF File 
Download CCD File 
A
(6AR,12AR)-6H-[1,3]DIOXOLO[5,6][1]BENZOFURO[3,2-C]CHROMENE-3,6A(12AH)-DIOL
C16 H12 O6
GLMPLZUBQDAZEN-CVEARBPZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.217α = 90.00
b = 71.217β = 90.00
c = 188.907γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2014-11-12
    Type: Structure summary