3D2H | pdb_00003d2h

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

PDB DOI: https://doi.org/10.2210/pdb3D2H/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.186 (Depositor), 0.178 (DCC)
R-Value Work:
0.155 (Depositor), 0.146 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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

PubMed: 18953357 Search on PubMed
DOI: https://doi.org/10.1038/nchembio.123
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 62.93 kDa
Atom Count: 5,070
Modeled Residue Count: 498
Deposited Residue Count: 538
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30986
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	6		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G60005GQ GlyCosmos: G60005GQ GlyGen: G60005GQ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FSH Query on FSH Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth 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		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.186 (Depositor), 0.178 (DCC)
R-Value Work: 0.155 (Depositor), 0.146 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.913	α = 90
b = 94.842	β = 100.31
c = 63.977	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-10-28

Deposition Author(s):

Revision History (Full details and data files)

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