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- PDB-5nzg: Crystal structure of UDP-glucose pyrophosphorylase S374W mutant f... -

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Basic information

Entry
Database: PDB / ID: 5nzg
TitleCrystal structure of UDP-glucose pyrophosphorylase S374W mutant from Leishmania major in complex with UDP-glucose
ComponentsUDP-glucose pyrophosphorylase
KeywordsTRANSFERASE / NTP-transferase / Pathogen / Allostery / Catalysis
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / ciliary plasm / nuclear lumen / glycogen metabolic process / cytoplasm / cytosol
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex ...UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCramer, J.T. / Fuehring, J.I. / Baruch, P. / Bruetting, C. / Hesse, R. / Knoelker, H.-J. / Gerardy-Schahn, R. / Fedorov, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGZ: FE 1510/2-1 Germany
CitationJournal: Acs Catalysis / Year: 2018
Title: Decoding Allosteric Networks in Biocatalysts: Rational Approach to Therapies and Biotechnologies
Authors: Cramer, J.T. / Fuehring, J.I. / Baruch, P. / Bruetting, C. / Knoelker, H.-J. / Gerardy-Schahn, R. / Fedorov, R.
History
DepositionMay 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucose pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,52715
Polymers56,1541
Non-polymers1,37314
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint33 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.500, 89.800, 137.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-958-

HOH

21A-1048-

HOH

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Components

#1: Protein UDP-glucose pyrophosphorylase


Mass: 56153.902 Da / Num. of mol.: 1 / Mutation: S374W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: UGP, LMJF_18_0990 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4QDU3, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.63 % / Mosaicity: 0.14 °
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 24% PEG 3350, 100 mM Bis-Tris pH 6.8, 0.2 M Li2SO4, 2 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.5→45.82 Å / Num. obs: 78616 / % possible obs: 99.6 % / Redundancy: 13.11 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.022 / Net I/σ(I): 23.25
Reflection shellMean I/σ(I) obs: 2.88 / Num. unique all: 13410 / Rsym value: 0.354 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SADABSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2M2A

2m2a


Resolution: 1.6→44.973 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.34
RfactorNum. reflection% reflection
Rfree0.2473 3260 5.02 %
Rwork0.2193 --
obs0.2206 64977 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→44.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 88 417 4235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023846
X-RAY DIFFRACTIONf_angle_d0.4465215
X-RAY DIFFRACTIONf_dihedral_angle_d15.6281410
X-RAY DIFFRACTIONf_chiral_restr0.04596
X-RAY DIFFRACTIONf_plane_restr0.003669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62390.36371400.33832693X-RAY DIFFRACTION100
1.6239-1.64930.31671370.32312606X-RAY DIFFRACTION100
1.6493-1.67630.35131590.32972673X-RAY DIFFRACTION100
1.6763-1.70520.33331420.31812637X-RAY DIFFRACTION100
1.7052-1.73620.37661380.30782650X-RAY DIFFRACTION100
1.7362-1.76960.3451410.29422692X-RAY DIFFRACTION100
1.7696-1.80570.28731340.28992663X-RAY DIFFRACTION100
1.8057-1.8450.2771500.26532622X-RAY DIFFRACTION100
1.845-1.88790.28711440.26372669X-RAY DIFFRACTION100
1.8879-1.93510.28981530.25062666X-RAY DIFFRACTION100
1.9351-1.98750.29291610.2492637X-RAY DIFFRACTION100
1.9875-2.04590.24441230.25232667X-RAY DIFFRACTION100
2.0459-2.1120.27991380.22832675X-RAY DIFFRACTION100
2.112-2.18750.29381340.23092670X-RAY DIFFRACTION100
2.1875-2.2750.2441380.22972691X-RAY DIFFRACTION100
2.275-2.37860.26191630.23662661X-RAY DIFFRACTION100
2.3786-2.5040.26821400.22422691X-RAY DIFFRACTION100
2.504-2.66080.27211420.2262675X-RAY DIFFRACTION100
2.6608-2.86620.21481380.21752709X-RAY DIFFRACTION100
2.8662-3.15460.22011470.20832708X-RAY DIFFRACTION100
3.1546-3.61090.20751490.19252709X-RAY DIFFRACTION100
3.6109-4.54870.21661270.17292776X-RAY DIFFRACTION100
4.5487-44.99090.20121220.18372877X-RAY DIFFRACTION100

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