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- PDB-4j18: Crystal structure of H191L mutant of UDP-glucose pyrophosphorylas... -

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Basic information

Entry
Database: PDB / ID: 4j18
TitleCrystal structure of H191L mutant of UDP-glucose pyrophosphorylase from Leishmania major
ComponentsUDP-glucose pyrophosphorylaseUTP—glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / Rossmann-like alpha/beta/alpha sandwich fold of catalytic domain / nucleotidyltransferase / UTP / Glc-1-P
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / nuclear lumen / ciliary plasm / glycogen metabolic process / cytosol / cytoplasm
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
UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFuehring, J.I. / Routier, F.H. / Lamerz, A.-C. / Baruch, P. / Gerardy-Schahn, R. / Fedorov, R.
CitationJournal: ACS CATALYSIS / Year: 2013
Title: Catalytic Mechanism and Allosteric Regulation of UDP-Glucose Pyrophosphorylase from Leishmania major
Authors: Fuehring, J.I. / Routier, F.H. / Lamerz, A.-C. / Baruch, P. / Gerardy-Schahn, R. / Fedorov, R.
History
DepositionFeb 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucose pyrophosphorylase


Theoretical massNumber of molelcules
Total (without water)56,0301
Polymers56,0301
Non-polymers00
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.310, 101.310, 71.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein UDP-glucose pyrophosphorylase / UTP—glucose-1-phosphate uridylyltransferase


Mass: 56029.781 Da / Num. of mol.: 1 / Mutation: H191L
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 3.29 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 10% v/v glycerol, 0.05 M citrate buffer, 1.1 M sodium citrate , pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91985 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2012
RadiationMonochromator: Liquid nitrogen cooled channel-cut silicon monochromator.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91985 Å / Relative weight: 1
ReflectionResolution: 2.35→19.5 Å / Num. all: 30457 / Num. obs: 30206 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 38.1 Å2 / Rsym value: 0.104 / Net I/σ(I): 9.8
Reflection shellResolution: 2.35→2.4 Å / % possible all: 98.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
REFMAC5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OEF

2oef


Resolution: 2.35→19.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.23221 1511 RANDOM
Rwork0.17805 --
all0.18075 30206 -
obs0.18075 30206 -
Refinement stepCycle: LAST / Resolution: 2.35→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 0 309 4053

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