4EVI | pdb_00004evi

Crystal Structure Analysis of Coniferyl Alcohol 9-O-Methyltransferase from Linum Nodiflorum in Complex with Coniferyl Alcohol 9-Methyl Ether and S -Adenosyl-L-Homocysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.203 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of coniferyl alcohol 9-O-methyltransferase from Linum nodiflorum reveals a novel active-site environment.

Wolters, S.Neeb, M.Berim, A.Schulze Wischeler, J.Petersen, M.Heine, A.

(2013) Acta Crystallogr D Biol Crystallogr 69: 888-900

  • DOI: https://doi.org/10.1107/S0907444913002874
  • Primary Citation Related Structures: 
    4E70, 4EMS, 4EVI

  • PubMed Abstract: 

    Coniferyl alcohol 9-O-methyltransferase from Linum nodiflorum (Linaceae) catalyzes the unusual methylation of the side-chain hydroxyl group of coniferyl alcohol. The protein was heterologously expressed in Escherichia coli as a hexahistidine derivative and purified for crystallization. Diffracting crystals were obtained of the pure protein and of its selenomethionine derivative, as well as of complexes with coniferyl alcohol and with S-adenosyl-L-homocysteine together with coniferyl alcohol 9-O-methyl ether (PDB entries 4ems, 4e70 and 4evi, respectively). The X-ray structures show that the phenylpropanoid binding mode differs from other phenylpropanoid O-methyltransferases such as caffeic acid O-methyltransferase. Moreover, the active site lacks the usually conserved and catalytic histidine residue and thus implies a different reaction mode for methylation. Site-directed mutagenesis was carried out to identify critical amino acids. The binding order of coniferyl alcohol and S-adenosyl-L-methionine was investigated by isothermal titration calorimetry experiments.


  • Organizational Affiliation
    • Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Deutschhausstrasse 17A, D-35037 Marburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 87.98 kDa 
  • Atom Count: 6,145 
  • Modeled Residue Count: 714 
  • Deposited Residue Count: 776 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coniferyl alcohol 9-O-methyltransferase
A, B
388Linum nodiflorumMutation(s): 0 
Gene Names: CA9OMT
UniProt
Find proteins for A6XNE6 (Linum nodiflorum)
Explore A6XNE6 
Go to UniProtKB:  A6XNE6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6XNE6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH

Query on SAH



Download:Ideal Coordinates CCD File
C [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
C9M

Query on C9M



Download:Ideal Coordinates CCD File
D [auth A]2-methoxy-4-[(1E)-3-methoxyprop-1-en-1-yl]phenol
C11 H14 O3
SBENKNZHVXGNTP-ONEGZZNKSA-N
N7I

Query on N7I



Download:Ideal Coordinates CCD File
F [auth B]4-[(1E)-3-hydroxyprop-1-en-1-yl]-2-methoxyphenol
C10 H12 O3
JMFRWRFFLBVWSI-NSCUHMNNSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
H [auth B],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.203 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.842α = 90
b = 105.042β = 90
c = 108.983γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description