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- PDB-5u6s: Crystal structure of UDP-glucosyltransferase, UGT74F2, with UDP a... -

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Basic information

Entry
Database: PDB / ID: 5u6s
TitleCrystal structure of UDP-glucosyltransferase, UGT74F2, 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 / positive regulation of seed germination / benzoate metabolic process / salicylic acid 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 / positive regulation of seed germination / benzoate metabolic process / salicylic acid 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 / Resolution: 1.996 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
DepositionDec 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)103,89910
Polymers101,6432
Non-polymers2,2558
Water2,720151
1
A: UDP-glycosyltransferase 74F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9495
Polymers50,8221
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)51,9495
Polymers50,8221
Non-polymers1,1284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.147, 87.249, 162.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 50821.621 Da / Num. of mol.: 2
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


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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, 155 molecules

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


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
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: 0.92024 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92024 Å / Relative weight: 1
ReflectionResolution: 1.996→50 Å / Num. obs: 120959 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 35.589470155 Å2 / Rsym value: 0.086 / Net I/σ(I): 38.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.996→37.544 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 6131 5.07 %
Rwork0.1844 --
obs0.1871 120959 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.996→37.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7074 0 136 151 7361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097396
X-RAY DIFFRACTIONf_angle_d1.04210048
X-RAY DIFFRACTIONf_dihedral_angle_d4.4314322
X-RAY DIFFRACTIONf_chiral_restr0.0551126
X-RAY DIFFRACTIONf_plane_restr0.0081266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9962-2.01880.34061840.32553630X-RAY DIFFRACTION93
2.0188-2.04260.35152050.32723820X-RAY DIFFRACTION100
2.0426-2.06750.3351820.31043829X-RAY DIFFRACTION100
2.0675-2.09370.33532160.30063859X-RAY DIFFRACTION100
2.0937-2.12120.30861960.28333814X-RAY DIFFRACTION100
2.1212-2.15030.33542130.27663808X-RAY DIFFRACTION100
2.1503-2.1810.33362090.27413856X-RAY DIFFRACTION100
2.181-2.21350.32182250.26143790X-RAY DIFFRACTION100
2.2135-2.24810.26352090.24513867X-RAY DIFFRACTION100
2.2481-2.2850.3231700.24283804X-RAY DIFFRACTION100
2.285-2.32440.28872350.233863X-RAY DIFFRACTION100
2.3244-2.36660.27142240.23643781X-RAY DIFFRACTION100
2.3666-2.41210.30052210.22933871X-RAY DIFFRACTION100
2.4121-2.46140.30772190.22663784X-RAY DIFFRACTION100
2.4614-2.51490.25541780.20353866X-RAY DIFFRACTION100
2.5149-2.57340.24012090.20543852X-RAY DIFFRACTION100
2.5734-2.63770.27031840.19563848X-RAY DIFFRACTION100
2.6377-2.7090.27722080.19883853X-RAY DIFFRACTION100
2.709-2.78870.26832270.20053788X-RAY DIFFRACTION100
2.7887-2.87870.25792330.19553812X-RAY DIFFRACTION100
2.8787-2.98150.27551790.20153850X-RAY DIFFRACTION100
2.9815-3.10080.29272320.20623861X-RAY DIFFRACTION100
3.1008-3.24190.22351910.20013827X-RAY DIFFRACTION100
3.2419-3.41270.24361820.19653868X-RAY DIFFRACTION100
3.4127-3.62630.22871910.18353879X-RAY DIFFRACTION100
3.6263-3.90610.22522170.15973782X-RAY DIFFRACTION100
3.9061-4.29860.17071960.13793847X-RAY DIFFRACTION100
4.2986-4.91950.16622010.12083846X-RAY DIFFRACTION100
4.9195-6.19350.2012130.13823818X-RAY DIFFRACTION100
6.1935-37.55090.18391820.13823855X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.0188 Å / Origin y: -8.2719 Å / Origin z: 17.9445 Å
111213212223313233
T0.2049 Å2-0.005 Å2-0.018 Å2-0.2275 Å2-0.0152 Å2--0.237 Å2
L0.0192 °2-0.1885 °20.1034 °2-0.3704 °2-0.2867 °2--0.4592 °2
S-0.0225 Å °-0.0167 Å °0.0336 Å °0.0141 Å °-0.0013 Å °-0.0173 Å °0.0197 Å °-0.0114 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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