3D2H

Structure of berberine bridge enzyme from Eschscholzia californica, monoclinic crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A concerted mechanism for berberine bridge enzyme

Winkler, A.Lyskowski, A.Riedl, S.Puhl, M.Kutchan, T.M.Macheroux, P.Gruber, K.

(2008) Nat.Chem.Biol. 4: 739-741

  • DOI: 10.1038/nchembio.123
  • Primary Citation of Related Structures:  3D2D, 3D2J

  • PubMed Abstract: 
  • Berberine bridge enzyme catalyzes the conversion of (S)-reticuline to (S)-scoulerine by formation of a carbon-carbon bond between the N-methyl group and the phenolic ring. We elucidated the structure of berberine bridge enzyme from Eschscholzia calif ...

    Berberine bridge enzyme catalyzes the conversion of (S)-reticuline to (S)-scoulerine by formation of a carbon-carbon bond between the N-methyl group and the phenolic ring. We elucidated the structure of berberine bridge enzyme from Eschscholzia californica and determined the kinetic rates for three active site protein variants. Here we propose a catalytic mechanism combining base-catalyzed proton abstraction with concerted carbon-carbon coupling accompanied by hydride transfer from the N-methyl group to the N5 atom of the FAD cofactor.


    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
berberine bridge-forming enzyme
A
538Eschscholzia californicaGene Names: BBE1
EC: 1.21.3.3
Find proteins for P30986 (Eschscholzia californica)
Go to UniProtKB:  P30986
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FSH
Query on FSH

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Download CCD File 
A
(2R,3S,4S)-5-[(4R)-6',7'-dimethyl-2,3',5-trioxo-1'H-spiro[imidazolidine-4,2'-quinoxalin]-4'(3'H)-yl]-2,3,4-trihydroxypentyl-adenosine diphosphate
C27 H35 N9 O16 P2
HUPQKJNMCVRMPP-QUWWARRSSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.155 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.913α = 90.00
b = 94.842β = 100.31
c = 63.977γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MAR345dtbdata collection
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance