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- PDB-5nzi: Crystal structure of UDP-glucose pyrophosphorylase S374F mutant f... -

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Basic information

Entry
Database: PDB / ID: 5nzi
TitleCrystal structure of UDP-glucose pyrophosphorylase S374F 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: 2.05 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)56,8675
Polymers56,1151
Non-polymers7534
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint9 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.390, 88.180, 137.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein UDP-glucose pyrophosphorylase


Mass: 56114.863 Da / Num. of mol.: 1 / Mutation: S374F
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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
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 Å
DetectorType: DECTRIS PILATUS 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: 2.05→50 Å / Num. obs: 30193 / % possible obs: 98.5 % / Redundancy: 13.43 % / Rsym value: 0.055 / Net I/σ(I): 10.49
Reflection shellResolution: 2.05→2.15 Å / Mean I/σ(I) obs: 2.24 / Num. unique all: 3929 / Rsym value: 0.421 / % possible all: 97.7

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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: 2.05→44.756 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1565 5.19 %
Rwork0.188 --
obs0.1909 30132 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→44.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 48 187 3962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133848
X-RAY DIFFRACTIONf_angle_d1.2255212
X-RAY DIFFRACTIONf_dihedral_angle_d14.6852316
X-RAY DIFFRACTIONf_chiral_restr0.062596
X-RAY DIFFRACTIONf_plane_restr0.008669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11620.35461320.30342554X-RAY DIFFRACTION98
2.1162-2.19180.36221320.27722538X-RAY DIFFRACTION98
2.1918-2.27960.33411280.2612554X-RAY DIFFRACTION98
2.2796-2.38330.38091470.2582563X-RAY DIFFRACTION98
2.3833-2.50890.28011370.24342546X-RAY DIFFRACTION98
2.5089-2.66610.31311290.23012594X-RAY DIFFRACTION98
2.6661-2.87190.29211690.23162563X-RAY DIFFRACTION99
2.8719-3.16090.29621440.21132609X-RAY DIFFRACTION99
3.1609-3.61810.22041530.17992624X-RAY DIFFRACTION99
3.6181-4.55770.19971410.13822671X-RAY DIFFRACTION99
4.5577-44.76620.17191530.14392751X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5612-1.67960.70361.5888-0.32912.1966-0.0478-0.1717-0.3047-0.0890.0250.2060.0156-0.29660.00750.2280.01140.00910.2429-0.02070.31319.345430.634254.8377
23.23580.9647-0.14911.6565-0.54094.06310.34750.52050.2747-0.5118-0.2547-0.252-0.93360.4318-0.07140.53870.0393-0.03590.420.08450.286425.467151.116940.6107
34.0426-0.2473-0.35183.3140.38443.85210.05410.35230.7253-0.2118-0.0986-0.5917-1.09370.89420.01960.5984-0.167-0.02890.54520.1210.415132.376853.040947.421
43.087-1.2278-0.1071.65060.25032.48320.18730.3374-0.3769-0.1725-0.27620.3279-0.1147-0.31850.09770.24780.0113-0.05880.2167-0.03730.295217.494835.064449.7731
51.4184-0.3345-1.03790.78790.35371.94340.30221.0077-0.0393-0.3627-0.34750.148-0.6257-0.54980.05350.49890.2301-0.10530.8492-0.02340.395519.23143.226526.8166
64.71190.2327-0.36211.5835-0.27791.75220.22691.1281-0.0859-0.6104-0.5582-0.0447-0.1175-0.25250.23660.61910.3268-0.10411.5077-0.07840.423821.842537.95249.2131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 69 )
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 157 )
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 361 )
5X-RAY DIFFRACTION5chain 'A' and (resid 362 through 456 )
6X-RAY DIFFRACTION6chain 'A' and (resid 457 through 488 )

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