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- PDB-2vch: Characterization and engineering of the bifunctional N- and O- gl... -

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Basic information

Entry
Database: PDB / ID: 2vch
TitleCharacterization and engineering of the bifunctional N- and O- glucosyltransferase involved in xenobiotic metabolism in plants
ComponentsHYDROQUINONE GLUCOSYLTRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / N-GLUCOSYLTRANSFERASE / UDP-GLUCOSE-DEPENDENT / PLANT GLYCOSYLTRANSFERASE / N-GLYCOSYLATION / O-GLYCOSYLATION / S-GLUCOSYLTRANSFERASE / O- GLUCOSYLTRANSFERASE
Function / homology
Function and homology information


hydroquinone glucosyltransferase / hydroquinone glucosyltransferase activity / lignin biosynthetic process / UDP-glucosyltransferase activity / UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / xenobiotic catabolic process / xenobiotic metabolic process / response to toxic substance
Similarity search - Function
UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 72B1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBrazier-Hicks, M. / Offen, W.A. / Gershater, M.C. / Revett, T.J. / Lim, E.K. / Bowles, D.J. / Davies, G.J. / Edwards, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Characterization and Engineering of the Bifunctional N- and O-Glucosyltransferase Involved in Xenobiotic Metabolism in Plants.
Authors: Brazier-Hicks, M. / Offen, W.A. / Gershater, M.C. / Revett, T.J. / Lim, E.K. / Bowles, D.J. / Davies, G.J. / Edwards, R.
History
DepositionSep 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROQUINONE GLUCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7698
Polymers52,9931
Non-polymers7777
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.680, 94.006, 56.992
Angle α, β, γ (deg.)90.00, 110.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HYDROQUINONE GLUCOSYLTRANSFERASE / ARBUTIN SYNTHASE / UGT72B1


Mass: 52992.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET-30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER
References: UniProt: Q9M156, hydroquinone glucosyltransferase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 23 % (W/V) PEG 3350, 0.1 M MMT (MALIC ACID, MES, TRIS BUFFER) PH 8.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.45→53.45 Å / Num. obs: 83274 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.9
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ACV

1acv


Resolution: 1.45→53.45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.951 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5, 50, 251-255, 318-319, 477-480 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4153 5 %RANDOM
Rwork0.178 ---
obs0.179 78900 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.02 Å2
2--0.72 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.45→53.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3570 0 49 444 4063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223824
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9955215
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7125495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07623.377154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74915649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3121527
X-RAY DIFFRACTIONr_chiral_restr0.1030.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022871
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21955
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22621
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2356
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1111.52421
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69423851
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.41331563
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6274.51346
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 293
Rwork0.262 5767

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