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- PDB-7vek: Crystal structure of Phytolacca americana UGT3 with capsaicin and... -

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Basic information

Entry
Database: PDB / ID: 7vek
TitleCrystal structure of Phytolacca americana UGT3 with capsaicin and UDP-2fluoroglucose
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / UGT / glycosyltransferase / capsaicin / UDP-2FGlc
Function / homology
Function and homology information


UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases
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
Chem-4DY / : / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / Chem-U2F / Glycosyltransferase
Similarity search - Component
Biological speciesPhytolacca americana (American pokeweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMaharjan, R. / Fukuda, Y. / Nakayama, T. / Nakayama, T. / Hamada, H. / Ozaki, S. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural basis for substrate recognition in the Phytolacca americana glycosyltransferase PaGT3.
Authors: Maharjan, R. / Fukuda, Y. / Nakayama, T. / Nakayama, T. / Hamada, H. / Ozaki, S.I. / Inoue, T.
History
DepositionSep 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0057
Polymers115,2602
Non-polymers1,7455
Water00
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5014
Polymers57,6301
Non-polymers8723
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-5 kcal/mol
Surface area19590 Å2
MethodPISA
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5033
Polymers57,6301
Non-polymers8742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-5 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.276, 103.022, 109.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNILEILE(chain 'A' and (resid 7 through 54 or resid 62 through 321 or resid 331 through 484))AA7 - 5427 - 74
12SERSERARGARG(chain 'A' and (resid 7 through 54 or resid 62 through 321 or resid 331 through 484))AA62 - 25482 - 274
13HISHISASNASN(chain 'A' and (resid 7 through 54 or resid 62 through 321 or resid 331 through 484))AA271 - 321291 - 341
14ASPASPHISHIS(chain 'A' and (resid 7 through 54 or resid 62 through 321 or resid 331 through 484))AA331 - 484351 - 504
21GLNGLNILEILE(chain 'B' and (resid 7 through 254 or resid 271 through 484))BB7 - 5427 - 74
22SERSERARGARG(chain 'B' and (resid 7 through 254 or resid 271 through 484))BB62 - 25482 - 274
23HISHISASNASN(chain 'B' and (resid 7 through 254 or resid 271 through 484))BB271 - 321291 - 341
24ASPASPHISHIS(chain 'B' and (resid 7 through 254 or resid 271 through 484))BB331 - 484351 - 504

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Components

#1: Protein Glycosyltransferase


Mass: 57629.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytolacca americana (American pokeweed)
Gene: PaGT3 / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B5MGN9, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O6
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23FN2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-4DY / (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide / Capsaicin / 8-Methyl-N-vanillyl-trans-6-nonenamide / NGX-4010


Mass: 305.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H27NO3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.15-0.20 M potassium acetate 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 33493 / % possible obs: 99.59 % / Redundancy: 6.8 % / Biso Wilson estimate: 55.92 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07 / Net I/σ(I): 17.86
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.12 / Num. unique obs: 3286 / CC1/2: 0.98 / Rpim(I) all: 0.24 / Rrim(I) all: 0.64 / % possible all: 99.36

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZY

6lzy


Resolution: 2.6→46.62 Å / SU ML: 0.4288 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.9987
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 1638 4.9 %
Rwork0.2045 31805 -
obs0.207 33443 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.94 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7249 0 113 0 7362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417541
X-RAY DIFFRACTIONf_angle_d0.715910198
X-RAY DIFFRACTIONf_chiral_restr0.04661111
X-RAY DIFFRACTIONf_plane_restr0.00431284
X-RAY DIFFRACTIONf_dihedral_angle_d24.78742767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.41791370.32672572X-RAY DIFFRACTION97.9
2.67-2.760.30711560.28882580X-RAY DIFFRACTION99.6
2.76-2.860.37791510.27432611X-RAY DIFFRACTION99.46
2.86-2.970.321440.26252594X-RAY DIFFRACTION99.74
2.97-3.110.30181160.25392661X-RAY DIFFRACTION99.86
3.11-3.270.34311160.25292648X-RAY DIFFRACTION99.75
3.27-3.480.28271280.23252648X-RAY DIFFRACTION99.64
3.48-3.750.25411240.21322634X-RAY DIFFRACTION99.67
3.75-4.120.22971420.19352685X-RAY DIFFRACTION99.72
4.12-4.720.22621320.16762664X-RAY DIFFRACTION99.79
4.72-5.940.23311400.17932705X-RAY DIFFRACTION99.79
5.94-46.620.20391520.15912803X-RAY DIFFRACTION98.93

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