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- PDB-5v2j: Crystal structure of UDP-glucosyltransferase, UGT74F2 (T15S), wit... -

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Basic information

Entry
Database: PDB / ID: 5v2j
TitleCrystal structure of UDP-glucosyltransferase, UGT74F2 (T15S), with UDP and 2-bromobenzoic acid
ComponentsUDP-glycosyltransferase 74F2
KeywordsTRANSFERASE / UDP-glucosyltransferase / Salicylic acid / Salicylic acid glucoside / Salicylic acid glucose ester
Function / homology
Function and homology information


para-aminobenzoic acid metabolic process / salicylic acid glucosyltransferase (ester-forming) activity / salicylic acid glucosyltransferase (glucoside-forming) activity / benzoic acid glucosyltransferase activity / UDP-glucose:4-aminobenzoate acylglucosyltransferase activity / nicotinate-O-glucosyltransferase activity / salicylic acid metabolic process / positive regulation of seed germination / benzoate metabolic process / UDP-glucosyltransferase activity ...para-aminobenzoic acid metabolic process / salicylic acid glucosyltransferase (ester-forming) activity / salicylic acid glucosyltransferase (glucoside-forming) activity / benzoic acid glucosyltransferase activity / UDP-glucose:4-aminobenzoate acylglucosyltransferase activity / nicotinate-O-glucosyltransferase activity / salicylic acid metabolic process / positive regulation of seed germination / benzoate metabolic process / UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / cytosol
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
beta-laminaribiose / 2-bromobenzoic acid / beta-D-glucopyranose / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 74F2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGeorge Thompson, A.M. / Iancu, C.V. / Dean, J.V. / Choe, J.
CitationJournal: Sci Rep / Year: 2017
Title: Differences in salicylic acid glucose conjugations by UGT74F1 and UGT74F2 from Arabidopsis thaliana.
Authors: George Thompson, A.M. / Iancu, C.V. / Neet, K.E. / Dean, J.V. / Choe, J.Y.
History
DepositionMar 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glycosyltransferase 74F2
B: UDP-glycosyltransferase 74F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,87010
Polymers101,6152
Non-polymers2,2558
Water3,081171
1
A: UDP-glycosyltransferase 74F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9355
Polymers50,8081
Non-polymers1,1284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-glycosyltransferase 74F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9355
Polymers50,8081
Non-polymers1,1284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.224, 87.410, 162.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UDP-glycosyltransferase 74F2 / AtSGT1 / Salicylic acid glucosyltransferase 1


Mass: 50807.594 Da / Num. of mol.: 2 / Mutation: T15S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UGT74F2, GT, SAGT1, SGT1, At2g43820, F18O19.7 / Production host: Escherichia coli (E. coli)
References: UniProt: O22822, Transferases; Glycosyltransferases; Hexosyltransferases

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(1+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 175 molecules

#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-7WV / 2-bromobenzoic acid


Mass: 201.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5BrO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22-26 %(w/v) PEG3350, 0.2 M ammonium acetate, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.99187 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 90391 / % possible obs: 99.4 % / Redundancy: 5.2 % / Net I/σ(I): 19.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2666: ???)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U6S

5u6s


Resolution: 1.8→42.211 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 4282 4.94 %
Rwork0.2023 --
obs0.2047 86654 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→42.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7072 0 136 171 7379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087394
X-RAY DIFFRACTIONf_angle_d0.91410044
X-RAY DIFFRACTIONf_dihedral_angle_d4.144322
X-RAY DIFFRACTIONf_chiral_restr0.0531124
X-RAY DIFFRACTIONf_plane_restr0.0061266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.34761590.35232679X-RAY DIFFRACTION98
1.8205-1.84190.38821410.34812650X-RAY DIFFRACTION99
1.8419-1.86430.39161310.34512760X-RAY DIFFRACTION99
1.8643-1.88790.36231340.34142656X-RAY DIFFRACTION99
1.8879-1.91280.38421390.32372715X-RAY DIFFRACTION99
1.9128-1.9390.37761500.31572699X-RAY DIFFRACTION99
1.939-1.96670.34971500.30752691X-RAY DIFFRACTION100
1.9667-1.9960.32111530.28912702X-RAY DIFFRACTION100
1.996-2.02720.29021390.2722717X-RAY DIFFRACTION100
2.0272-2.06050.30511470.26792731X-RAY DIFFRACTION100
2.0605-2.0960.32881330.2552735X-RAY DIFFRACTION100
2.096-2.13410.28711520.24272724X-RAY DIFFRACTION100
2.1341-2.17510.31261340.23262753X-RAY DIFFRACTION100
2.1751-2.21950.31171210.22752705X-RAY DIFFRACTION100
2.2195-2.26780.26751370.22192734X-RAY DIFFRACTION100
2.2678-2.32060.24561300.21692758X-RAY DIFFRACTION100
2.3206-2.37860.2771460.21962719X-RAY DIFFRACTION100
2.3786-2.44290.27411550.21942726X-RAY DIFFRACTION100
2.4429-2.51480.27561280.222772X-RAY DIFFRACTION100
2.5148-2.59590.29511280.2172757X-RAY DIFFRACTION100
2.5959-2.68870.28621450.22272733X-RAY DIFFRACTION100
2.6887-2.79630.31371450.21962772X-RAY DIFFRACTION100
2.7963-2.92350.26881390.22572766X-RAY DIFFRACTION100
2.9235-3.07760.29411520.2292747X-RAY DIFFRACTION100
3.0776-3.27040.26781460.21672778X-RAY DIFFRACTION100
3.2704-3.52280.27211520.20252769X-RAY DIFFRACTION100
3.5228-3.87710.22841460.1812806X-RAY DIFFRACTION100
3.8771-4.43760.17571430.152803X-RAY DIFFRACTION99
4.4376-5.58880.20191600.13972827X-RAY DIFFRACTION100
5.5888-42.22250.15591470.14632988X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.2914 Å / Origin y: -8.1544 Å / Origin z: 17.9883 Å
111213212223313233
T0.2113 Å2-0.0329 Å2-0.0273 Å2-0.2597 Å2-0.0251 Å2--0.2767 Å2
L0.0584 °2-0.4824 °20.246 °2-0.6509 °2-0.6094 °2--0.9766 °2
S-0.044 Å °-0.0055 Å °0.0447 Å °0.0222 Å °-0.0262 Å °-0.0458 Å °0.0977 Å °-0.0062 Å °0.0692 Å °
Refinement TLS groupSelection details: all

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