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- PDB-3fwa: Structure of berberine bridge enzyme, C166A variant in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3fwa
TitleStructure of berberine bridge enzyme, C166A variant in complex with (S)-reticuline
ComponentsReticuline oxidase
KeywordsFLAVOPROTEIN / BI-COVALENT FLAVINYLATION / N-GLYCOSYLATION / ALAKLOID BIOSYNTHESIS / OXIDOREDUCTASE / Alkaloid metabolism / Cytoplasmic vesicle / FAD / 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 / Oxygen oxidoreductases covalent FAD-binding site. / Berberine/berberine-like / Berberine and berberine like / 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 / Oxygen oxidoreductases covalent FAD-binding site. / Berberine/berberine-like / Berberine and berberine like / 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
FLAVIN-ADENINE DINUCLEOTIDE / (S)-reticuline / Reticuline oxidase
Similarity search - Component
Biological speciesEschscholzia californica (California poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.496 Å
AuthorsWinkler, A. / Macheroux, P. / Gruber, K.
Citation
Journal: to be published
Title: Structural roles of biocovalent flaninylation in berberine bridge enzyme
Authors: Winkler, A. / Motz, K. / Riedl, S. / Puhl, M. / Macheroux, P. / Gruber, K.
#1: Journal: Nat. Chem. Biol. / Year: 2008
Title: A concerted mechanism for berberine bridge enzyme.
Authors: Winkler, A. / Lyskowski, A. / Riedl, S. / Puhl, M. / Kutchan, T.M. / Macheroux, P. / Gruber, K.
History
DepositionJan 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_struct_special_symmetry / pdbx_validate_chiral / struct_asym / struct_conn / 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 / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticuline oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5416
Polymers55,5941
Non-polymers1,9475
Water11,512639
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.870, 68.870, 246.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1130-

HOH

Detailsbiological unit is the same as asymmetric unit.

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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: 55593.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eschscholzia californica (California poppy)
Gene: BBE1 / Plasmid: PPICZA / 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 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_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, 642 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-REN / (S)-reticuline / (1S)-1-(3-hydroxy-4-methoxybenzyl)-6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-ol


Mass: 329.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23NO4
#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.: 639 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M MAGNESIUMCHLORIDE, 30% PEG-4000, 0.1 M TRIS/HCL, pH 8.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.496→41.9 Å / Num. all: 95673 / Num. obs: 95673 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 12.78 Å2 / Rsym value: 0.053 / Net I/σ(I): 16.6
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.233 / % possible all: 91.5

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d2j

3d2j


Resolution: 1.496→41.892 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.914 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.177 4780 5 %random
Rwork0.162 ---
all0.162 95673 --
obs0.162 95673 98.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.894 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 91.87 Å2 / Biso mean: 18.992 Å2 / Biso min: 6 Å2
Baniso -1Baniso -2Baniso -3
1--1.854 Å2-0 Å2-0 Å2
2---1.854 Å2-0 Å2
3----1.466 Å2
Refinement stepCycle: LAST / Resolution: 1.496→41.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3925 0 131 639 4695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134429
X-RAY DIFFRACTIONf_angle_d1.0656066
X-RAY DIFFRACTIONf_chiral_restr0.067662
X-RAY DIFFRACTIONf_plane_restr0.005758
X-RAY DIFFRACTIONf_dihedral_angle_d18.2761628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.496-1.5130.2541160.2182092220871
1.513-1.5310.2261680.18830223190100
1.531-1.5490.2371520.17929693121100
1.549-1.5690.2051670.17730383205100
1.569-1.590.1741580.16229933151100
1.59-1.6110.1721670.1612982314999
1.611-1.6340.1811700.1593005317599
1.634-1.6590.181620.16629983160100
1.659-1.6850.1821520.15630293181100
1.685-1.7120.1691670.15430103177100
1.712-1.7420.1611490.14830343183100
1.742-1.7740.1651560.15130463202100
1.774-1.8080.1871600.15830113171100
1.808-1.8450.1691640.15729983162100
1.845-1.8850.1721610.15230303191100
1.885-1.9290.1681530.15630633216100
1.929-1.9770.1911450.14830633208100
1.977-2.030.1661410.14930713212100
2.03-2.090.1641540.15230393193100
2.09-2.1570.1651590.14730523211100
2.157-2.2340.1731330.15130823215100
2.234-2.3240.1751400.15530773217100
2.324-2.430.1871560.15930813237100
2.43-2.5580.1781740.16131033277100
2.558-2.7180.1751750.16530623237100
2.718-2.9280.1661580.16830983256100
2.928-3.2220.1651630.16131463309100
3.222-3.6880.1511970.14831353332100
3.688-4.6460.1561930.13731873380100
4.646-41.9080.1861700.1793377354799
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)
10.59890.0727-0.1860.7830.02970.2117-0.02230.1672-0.0851-0.1762-0.0357-0.08610.02550.0450.04360.11110.00850.00090.1698-0.00110.0898-18.1065-2.284-33.3374
20.49930.02350.13040.40650.18320.3420.03080.01250.00250.02810.0262-0.0255-0.02380.065-0.01830.0516-0.0081-0.00490.07050.01270.0443-16.98158.122-13.9443
31.39070.42520.05980.2974-0.35590.47540.0404-0.2118-0.02810.0271-0.02320.05420.0755-0.0147-0.02530.0978-0.009-0.01210.09430.00960.1032-27.3201-7.03884.3667
40.60640.3612-0.00270.3874-0.28470.44290.01810.0406-0.03850.00790.06460.02610.0386-0.0511-0.06720.074-0.0082-0.00270.09870.01320.0963-39.3335-4.1946-9.8936
50.4717-0.12820.23820.23250.04290.28440.02280.0780.0411-0.0546-0.01230.0769-0.0934-0.0744-0.02220.09410.0171-0.0050.11860.03470.0963-36.456511.6148-26.9372
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 245:350)
4X-RAY DIFFRACTION4(chain A and resid 351:456)
5X-RAY DIFFRACTION5(chain A and resid 457:522)

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