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- PDB-8yp3: Crystal structure of UDP-N-acetylglucosamine pyrophosphorylase fr... -

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Basic information

Entry
Database: PDB / ID: 8yp3
TitleCrystal structure of UDP-N-acetylglucosamine pyrophosphorylase from Spodoptera frugiperda in complex with UDP-GlcNAc
ComponentsUDP-N-acetylglucosamine diphosphorylase
KeywordsSUGAR BINDING PROTEIN / UDP-N-acetylglucosamine pyrophosphorylase / Spodoptera frugiperda / UDP-GlcNAc
Function / homologyUDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / Nucleotide-diphospho-sugar transferases / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine diphosphorylase
Function and homology information
Biological speciesSpodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsLu, Q. / Liu, T. / Zhou, Y. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Structure and Inhibition of Insect UDP- N -acetylglucosamine Pyrophosphorylase: A Key Enzyme in the Hexosamine Biosynthesis Pathway.
Authors: Lu, Q. / Zhou, Y. / Ding, Y. / Cui, Y. / Li, W. / Liu, T.
History
DepositionMar 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine diphosphorylase
B: UDP-N-acetylglucosamine diphosphorylase
C: UDP-N-acetylglucosamine diphosphorylase
D: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,83216
Polymers217,9214
Non-polymers2,91112
Water17,889993
1
A: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2084
Polymers54,4801
Non-polymers7283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2084
Polymers54,4801
Non-polymers7283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2084
Polymers54,4801
Non-polymers7283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2084
Polymers54,4801
Non-polymers7283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.734, 233.527, 98.063
Angle α, β, γ (deg.)90.000, 90.113, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
UDP-N-acetylglucosamine diphosphorylase


Mass: 54480.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Gene: SFRICE_001055 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2H1VI03, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical
ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 993 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris, pH 6.0, 200 mM (NH4)2SO4, 22% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.12→90.41 Å / Num. obs: 114563 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.2
Reflection shellResolution: 2.12→2.23 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 16936 / CC1/2: 0.82 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→29 Å / SU ML: 0.222 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2199 2001 1.75 %
Rwork0.1918 112441 -
obs0.1923 114442 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.89 Å2
Refinement stepCycle: LAST / Resolution: 2.12→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14772 0 180 993 15945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006515267
X-RAY DIFFRACTIONf_angle_d0.916120626
X-RAY DIFFRACTIONf_chiral_restr0.06052235
X-RAY DIFFRACTIONf_plane_restr0.00532673
X-RAY DIFFRACTIONf_dihedral_angle_d19.10555864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.28071450.25398178X-RAY DIFFRACTION99.94
2.17-2.230.2711450.23518052X-RAY DIFFRACTION99.99
2.23-2.30.23291130.23226648X-RAY DIFFRACTION81.16
2.3-2.370.26451440.21328091X-RAY DIFFRACTION99.98
2.37-2.450.25011440.21188164X-RAY DIFFRACTION99.95
2.45-2.550.28861460.21038123X-RAY DIFFRACTION100
2.55-2.670.27441410.21628141X-RAY DIFFRACTION99.98
2.67-2.810.2841460.2168109X-RAY DIFFRACTION99.94
2.81-2.990.2421460.21398138X-RAY DIFFRACTION99.96
2.99-3.220.25141440.2088160X-RAY DIFFRACTION99.94
3.22-3.540.21651440.19468166X-RAY DIFFRACTION99.96
3.54-4.050.20671480.16798113X-RAY DIFFRACTION99.94
4.05-5.10.15471470.15428202X-RAY DIFFRACTION99.95
5.1-290.191480.1788156X-RAY DIFFRACTION99.51

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