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- PDB-5u6m: Crystal structure of UDP-glucosyltransferase, UGT74F2, with UDP a... -

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Basic information

Entry
Database: PDB / ID: 5u6m
TitleCrystal structure of UDP-glucosyltransferase, UGT74F2, with UDP and salicylic acid
ComponentsUDP-glycosyltransferase 74F2
KeywordsTRANSFERASE / UDP-glucosyltransferase / salicylic acid / salicylic acid glucoside / salicylic acid 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-D-glucopyranose / 2-HYDROXYBENZOIC ACID / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 74F2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.568 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 1.1Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,0888
Polymers101,6432
Non-polymers1,4456
Water905
1
A: UDP-glycosyltransferase 74F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5444
Polymers50,8221
Non-polymers7223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-glycosyltransferase 74F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5444
Polymers50,8221
Non-polymers7223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.694, 87.681, 164.250
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

#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
#2: 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
#3: 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
#4: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
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: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 30702 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 68.6431469736 Å2 / Net I/σ(I): 0.086
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.7 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.568→43.841 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 1541 5.03 %
Rwork0.1876 --
obs0.1914 30628 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.568→43.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7060 0 92 5 7157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117334
X-RAY DIFFRACTIONf_angle_d1.2139965
X-RAY DIFFRACTIONf_dihedral_angle_d4.6484311
X-RAY DIFFRACTIONf_chiral_restr0.0621107
X-RAY DIFFRACTIONf_plane_restr0.0081264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5683-2.65120.36041240.2772428X-RAY DIFFRACTION93
2.6512-2.74590.34141390.26092618X-RAY DIFFRACTION99
2.7459-2.85580.36181500.25392601X-RAY DIFFRACTION99
2.8558-2.98580.37241300.24042633X-RAY DIFFRACTION99
2.9858-3.14320.30621380.23932629X-RAY DIFFRACTION99
3.1432-3.340.33251460.22862638X-RAY DIFFRACTION99
3.34-3.59780.32181250.21132652X-RAY DIFFRACTION100
3.5978-3.95960.23981450.18562654X-RAY DIFFRACTION99
3.9596-4.53210.2051400.15622694X-RAY DIFFRACTION100
4.5321-5.7080.24221500.16412709X-RAY DIFFRACTION100
5.708-43.84690.2241540.16512831X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 56.5102 Å / Origin y: 75.947 Å / Origin z: 59.1517 Å
111213212223313233
T0.4321 Å20.0634 Å20.0059 Å2-0.414 Å20.0224 Å2--0.5086 Å2
L0.4705 °20.0741 °2-0.6546 °2-0.4431 °20.4679 °2--2.0802 °2
S0.0443 Å °0.0206 Å °0.0454 Å °-0.0669 Å °0.0166 Å °0.035 Å °-0.0213 Å °-0.0763 Å °0.0136 Å °
Refinement TLS groupSelection details: all

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