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- PDB-3vte: Crystal structure of tetrahydrocannabinolic acid synthase from Ca... -

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Basic information

Entry
Database: PDB / ID: 3vte
TitleCrystal structure of tetrahydrocannabinolic acid synthase from Cannabis sativa
ComponentsTetrahydrocannabinolic acid synthase
KeywordsOXIDOREDUCTASE / BI-COVALENT FLAVINYLATION
Function / homology
Function and homology information


tetrahydrocannabinolic acid synthase / delta9-tetrahydrocannabinolate synthase activity / cannabinoid biosynthetic process / apoplast / terpenoid biosynthetic process / FAD binding
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / 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 ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / 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 / Tetrahydrocannabinolic acid synthase
Similarity search - Component
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsShoyama, Y. / Tamada, T. / Kurihara, K. / Takeuchi, A. / Taura, F. / Arai, S. / Blaber, M. / Shoyama, Y. / Morimoto, S. / Kuroki, R.
Citation
Journal: J.Mol.Biol. / Year: 2012
Title: Structure and function of 1-tetrahydrocannabinolic acid (THCA) synthase, the enzyme controlling the psychoactivity of Cannabis sativa
Authors: Shoyama, Y. / Tamada, T. / Kurihara, K. / Takeuchi, A. / Taura, F. / Arai, S. / Blaber, M. / Shoyama, Y. / Morimoto, S. / Kuroki, R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization of Delta1-tetrahydrocannabinolic acid (THCA) synthase from Cannabis sativa
Authors: Shoyama, Y. / Takeuchi, A. / Taura, F. / Tamada, T. / Adachi, M. / Kuroki, R. / Shoyama, Y. / Morimoto, S.
History
DepositionMay 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 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
Revision 1.4Oct 30, 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: Tetrahydrocannabinolic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8598
Polymers58,7461
Non-polymers2,1137
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)177.946, 177.946, 177.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#1: Protein Tetrahydrocannabinolic acid synthase


Mass: 58745.859 Da / Num. of mol.: 1 / Fragment: UNP residues 28-545
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cannabis sativa (plant) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): 7108 / References: UniProt: Q8GTB6
#2: 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.: 6
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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
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: 4 Å3/Da / Density % sol: 69.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.09M HEPES, 1.26M SODIUM CITRATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→44.5 Å / Num. obs: 25537 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 15.6 % / Rsym value: 0.088 / Net I/σ(I): 14.6
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 5.6 % / Rsym value: 0.371 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AXR

2axr


Resolution: 2.75→44.49 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / SU B: 26.579 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.425 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25039 1294 5.1 %RANDOM
Rwork0.19848 ---
obs0.20111 24099 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.129 Å2
Refinement stepCycle: LAST / Resolution: 2.75→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 137 51 4211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.9795810
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.715498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90224.171187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.46315706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2551516
X-RAY DIFFRACTIONr_chiral_restr0.1230.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213209
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8311.52493
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61824039
X-RAY DIFFRACTIONr_scbond_it2.16131788
X-RAY DIFFRACTIONr_scangle_it3.7114.51771
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 98 -
Rwork0.332 1734 -
obs--98.55 %
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)
12.16780.28150.13651.155-1.30542.8130.16230.18450.0426-0.1552-0.17430.36050.16440.03160.0120.17690.0283-0.03620.122-0.08290.125354.65366.678-48.297
20.2034-0.15430.07520.5491-0.12960.7167-0.01570.0576-0.03610.0670.05530.03410.02590.1246-0.03960.14350.0132-0.01510.1642-0.02340.140471.46154.849-28.365
30.8133-0.111-0.48880.42330.15070.96670.0308-0.0388-0.01490.0484-0.05020.14380.07090.01250.01930.1551-0.02260.01220.13620.01090.164960.36356.939-18.868
41.275-1.1511-0.22472.6108-0.75340.954-0.07020.0910.14540.26920.1465-0.067-0.1472-0.0138-0.07640.2348-0.0157-0.03090.1084-0.01640.111264.91879.182-24.963
52.4852-0.9072-0.26531.40030.03661.1749-0.14070.09650.3184-0.07560.1314-0.12830.3095-0.25440.00930.1476-0.0225-0.07250.1068-0.03830.232665.44658.347-28.757
60.40830.3848-0.11750.0083-0.1101-0.2180.0366-0.05410.2237-0.05050.01230.11680.17180.146-0.04890.3058-0.024-0.04730.2423-0.01350.05570.88759.501-28.873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 84
2X-RAY DIFFRACTION2A85 - 353
3X-RAY DIFFRACTION3A354 - 504
4X-RAY DIFFRACTION4A505 - 545
5X-RAY DIFFRACTION5A601 - 607
6X-RAY DIFFRACTION6A801 - 851

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