3D2J

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

• PDB DOI: https://doi.org/10.2210/pdb3D2J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Eschscholzia californica
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2008-05-08 Released: 2008-10-28 
• Deposition Author(s): Winkler, A., Lyskowski, A., Macheroux, P., Gruber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

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

• PubMed: 18953357 
• DOI: https://doi.org/10.1038/nchembio.123
• Primary Citation of Related Structures:  
  3D2D, 3D2H, 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.66 kDa 
• Atom Count: 4,567 
• Modelled Residue Count: 502 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
berberine bridge-forming enzyme	A	538	Eschscholzia californica	Mutation(s): 0  Gene Names: BBE1 EC: 1.21.3.3
UniProt
Find proteins for P30986 (Eschscholzia californica) Explore P30986  Go to UniProtKB:  P30986
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.52	α = 90
b = 68.52	β = 90
c = 246.278	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Winkler, A., Lyskowski, A., Macheroux, P., Gruber, K.

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary