3GSY

Structure of berberine bridge enzyme in complex with dehydroscoulerine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Berberine bridge enzyme catalyzes the six electron oxidation of (S)-reticuline to dehydroscoulerine.

Winkler, A.Puhl, M.Weber, H.Kutchan, T.M.Gruber, K.Macheroux, P.

(2009) Phytochemistry 70: 1092-1097

  • DOI: 10.1016/j.phytochem.2009.06.005

  • PubMed Abstract: 
  • Berberine bridge enzyme catalyzes the stereospecific oxidation and carbon-carbon bond formation of (S)-reticuline to (S)-scoulerine. In addition to this type of reactivity the enzyme can further oxidize (S)-scoulerine to the deeply red protoberberine ...

    Berberine bridge enzyme catalyzes the stereospecific oxidation and carbon-carbon bond formation of (S)-reticuline to (S)-scoulerine. In addition to this type of reactivity the enzyme can further oxidize (S)-scoulerine to the deeply red protoberberine alkaloid dehydroscoulerine albeit with a much lower rate of conversion. In the course of the four electron oxidation, no dihydroprotoberberine species intermediate was detectable suggesting that the second oxidation step leading to aromatization proceeds at a much faster rate. Performing the reaction in the presence of oxygen and under anoxic conditions did not affect the kinetics of the overall reaction suggesting no strict requirement for oxygen in the oxidation of the unstable dihydroprotoberberine intermediate. In addition to the kinetic characterization of this reaction we also present a structure of the enzyme in complex with the fully oxidized product. Combined with information available for the binding modes of (S)-reticuline and (S)-scoulerine a possible mechanism for the additional oxidation is presented. This is compared to previous reports of enzymes ((S)-tetrahydroprotoberberine oxidase and canadine oxidase) showing a similar type of reactivity in different plant species.


    Organizational Affiliation

    Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reticuline oxidase; Berberine bridge-forming enzyme
A
519Eschscholzia californicaGene Names: BBE1
EC: 1.21.3.3
Find proteins for P30986 (Eschscholzia californica)
Go to UniProtKB:  P30986
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DEH
Query on DEH

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A
2,9-dihydroxy-3,10-dimethoxy-5,6-dihydroisoquino[3,2-a]isoquinolinium
C19 H18 N O4
DRAPVRZDBZHUPL-UHFFFAOYSA-O
 Ligand Interaction
FAD
Query on FAD

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A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.940α = 90.00
b = 68.940β = 90.00
c = 247.260γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance