3C3Y

Crystal Structure of PFOMT, Phenylpropanoid and Flavonoid O-methyltransferase from M. crystallinum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.371 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Biochemical and Structural Analysis of Substrate Promiscuity in Plant Mg(2+)-Dependent O-Methyltransferases

Kopycki, J.G.Rauh, D.Chumanevich, A.A.Neumann, P.Vogt, T.Stubbs, M.T.

(2008) J.Mol.Biol. 378: 154-164

  • DOI: 10.1016/j.jmb.2008.02.019

  • PubMed Abstract: 
  • Plant S-adenosyl-l-methionine-dependent class I natural product O-methyltransferases (OMTs), related to animal catechol OMTs, are dependent on bivalent cations and strictly specific for the meta position of aromatic vicinal dihydroxy groups. While th ...

    Plant S-adenosyl-l-methionine-dependent class I natural product O-methyltransferases (OMTs), related to animal catechol OMTs, are dependent on bivalent cations and strictly specific for the meta position of aromatic vicinal dihydroxy groups. While the primary activity of these class I enzymes is methylation of caffeoyl coenzyme A OMTs, a distinct subset is able to methylate a wider range of substrates, characterized by the promiscuous phenylpropanoid and flavonoid OMT. The observed broad substrate specificity resides in two regions: the N-terminus and a variable insertion loop near the C-terminus, which displays the lowest degree of sequence conservation between the two subfamilies. Structural and biochemical data, based on site-directed mutagenesis and domain exchange between the two enzyme types, present evidence that only small topological changes among otherwise highly conserved 3-D structures are sufficient to differentiate between an enzymatic generalist and an enzymatic specialist in plant natural product methylation.


    Organizational Affiliation

    Institut für Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-methyltransferase
A, B
237Mesembryanthemum crystallinumMutation(s): 0 
EC: 2.1.1.104
Find proteins for Q6YI95 (Mesembryanthemum crystallinum)
Go to UniProtKB:  Q6YI95
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.371 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.890α = 90.00
b = 71.830β = 90.00
c = 128.120γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance