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- PDB-3gsy: Structure of berberine bridge enzyme in complex with dehydroscoulerine -

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Basic information

Entry
Database: PDB / ID: 3gsy
TitleStructure of berberine bridge enzyme in complex with dehydroscoulerine
ComponentsReticuline oxidase; Berberine bridge-forming enzyme
KeywordsOXIDOREDUCTASE / complex with dehydroscoulerine / bicovalent flavinylation / N-glycosylation / p-cresol methyl hydroxylase superfamily / Alkaloid metabolism / Cytoplasmic vesicle / FAD / Flavoprotein / Glycoprotein
Function / homology
Function and homology information


reticuline oxidase / reticuline oxidase activity / alkaloid metabolic process / FAD binding / cytoplasmic vesicle
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DEH / FLAVIN-ADENINE DINUCLEOTIDE / Reticuline oxidase
Similarity search - Component
Biological speciesEschscholzia californica (California poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.63 Å
AuthorsWinkler, A. / Macheroux, P. / Gruber, K.
CitationJournal: Phytochemistry / Year: 2009
Title: Berberine bridge enzyme catalyzes the six electron oxidation of (S)-reticuline to dehydroscoulerine.
Authors: Winkler, A. / Puhl, M. / Weber, H. / Kutchan, T.M. / Gruber, K. / Macheroux, P.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticuline oxidase; Berberine bridge-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8176
Polymers57,8751
Non-polymers1,9425
Water12,250680
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.940, 68.940, 247.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Reticuline oxidase; Berberine bridge-forming enzyme / BBE / Tetrahydroprotoberberine synthase


Mass: 57875.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eschscholzia californica (California poppy)
Gene: BBE1 / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: P30986, reticuline oxidase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 683 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-DEH / 2,9-dihydroxy-3,10-dimethoxy-5,6-dihydroisoquino[3,2-a]isoquinolinium


Mass: 324.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18NO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M MgCl2, 30% PEG-4000, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2008 / Details: mirrors
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. all: 76019 / Num. obs: 76019 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 13 % / Rsym value: 0.062 / Net I/σ(I): 18.4
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.481 / % possible all: 98.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
PHENIXphasing
RefinementStarting model: 3D2J

3d2j


Resolution: 1.63→45.35 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.912 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.185 3821 5.03 %random
Rwork0.162 ---
obs0.163 76019 99.77 %-
all-76019 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.01 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 114.47 Å2 / Biso mean: 23.506 Å2 / Biso min: 8.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å2-0 Å2
2--0.9 Å2-0 Å2
3----1.801 Å2
Refinement stepCycle: LAST / Resolution: 1.63→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3907 0 131 680 4718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124275
X-RAY DIFFRACTIONf_angle_d1.0955832
X-RAY DIFFRACTIONf_chiral_restr0.07637
X-RAY DIFFRACTIONf_plane_restr0.005729
X-RAY DIFFRACTIONf_dihedral_angle_d18.0921553
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.626-1.6460.2221330.2132489262294
1.646-1.6680.2571250.19726062731100
1.668-1.6910.2311430.18626532796100
1.691-1.7150.2271450.17626182763100
1.715-1.7410.2251390.16926432782100
1.741-1.7680.2071380.16926462784100
1.768-1.7970.1871320.16526132745100
1.797-1.8280.191360.15926422778100
1.828-1.8610.1621390.15426722811100
1.861-1.8970.1781500.15726182768100
1.897-1.9360.1751230.16226532776100
1.936-1.9780.1751530.15726442797100
1.978-2.0240.2191370.15626782815100
2.024-2.0740.1841360.15726532789100
2.074-2.130.181540.15826212775100
2.13-2.1930.1771350.15726752810100
2.193-2.2640.1961370.15426692806100
2.264-2.3450.1821450.15126742819100
2.345-2.4380.181350.15726992834100
2.438-2.5490.2021420.16326832825100
2.549-2.6840.1821490.16826702819100
2.684-2.8520.2011490.16527162865100
2.852-3.0720.1891640.16226842848100
3.072-3.3810.1841410.15327292870100
3.381-3.870.1711480.14327662914100
3.87-4.8750.1361600.13128022962100
4.875-45.3680.1831330.1692982311599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0337-0.0574-0.05880.96240.39150.81720.06580.3713-0.1396-0.2669-0.0356-0.09720.1170.2087-0.04970.16270.0474-0.00450.3082-0.02520.1425-18.5679-2.4512-33.3098
20.84820.04710.25360.64090.15510.98420.09770.07420.02770.02640.0235-0.0413-0.05590.1251-0.09250.0977-0.00730.0060.10830.00330.1085-17.02477.8603-14.0806
32.08380.61590.00920.4195-0.31860.7350.1018-0.2512-0.1240.0346-0.0570.03410.14820.0173-0.04450.1665-0.0162-0.02580.12160.00930.1477-27.6721-7.13134.5006
40.28980.53370.37580.59940.36160.93360.10570.0097-0.13480.00610.0721-0.02950.07180.1664-0.16440.1316-0.008-0.01540.19240.01450.1722-38.9664-5.7331-8.192
51.12190.3759-0.24740.6265-0.18250.77140.05420.1377-0.04220.05270.05460.05080.1108-0.073-0.08750.10240.0009-0.01550.12330.00680.1242-38.9225-3.3862-10.7396
60.7014-0.13160.1320.1233-0.08761.16290.11150.22920.1743-0.09560.00820.1367-0.2189-0.3023-0.13230.15560.06850.01540.18030.0810.1569-36.626712.2284-27.3067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 26:114)
2X-RAY DIFFRACTION2(chain A and resid 115:244)
3X-RAY DIFFRACTION3(chain A and resid 245:349)
4X-RAY DIFFRACTION4(chain A and resid 350:374)
5X-RAY DIFFRACTION5(chain A and resid 375:460)
6X-RAY DIFFRACTION6(chain A and resid 461:520)

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