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- PDB-8tg2: The crystal structure of the post-reactive state of UDP-sugar pyr... -

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Basic information

Entry
Database: PDB / ID: 8tg2
TitleThe crystal structure of the post-reactive state of UDP-sugar pyrophosphorylase from Leishmania major in complex with products UDP-Glucose and PPi
ComponentsUTP-monosaccharide-1-phosphate uridylyltransferase
KeywordsSUGAR BINDING PROTEIN / carbohydrate biosynthesis / nucleotidyltransferase / catalysis / molecular mechanism
Function / homologyUTP-monosaccharide-1-phosphate uridylyltransferase / UDP-sugar pyrophosphorylase / uridylyltransferase activity / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Nucleotide-diphospho-sugar transferases / PYROPHOSPHATE 2- / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP-monosaccharide-1-phosphate uridylyltransferase
Function and homology information
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPrakash, O. / Fuehring, J.I. / Baruch, P. / Routier, F.H. / Fedorov, R.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)FE 1510/2-1 Germany
European Union (EU)EU FP7, GA. 608295European Union
CitationJournal: To Be Published
Title: The post-reactive state structures of Leishmania major UDP-sugar pyrophosphorylase provide insights into the product release mechanism
Authors: Prakash, O. / Fuehring, J.I. / Baruch, P. / Routier, F.H. / Fedorov, R.
History
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UTP-monosaccharide-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8544
Polymers66,9361
Non-polymers9183
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.090, 121.900, 60.960
Angle α, β, γ (deg.)90.00, 105.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-967-

HOH

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Components

#1: Protein UTP-monosaccharide-1-phosphate uridylyltransferase


Mass: 66935.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: USP / Production host: Escherichia coli (E. coli)
References: UniProt: D3G6S4, UTP-monosaccharide-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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium acetate, 100 mM tri-sodium citrate, pH 5.4 - 5.6, and 15% - 17% polyethylene glycol-4000 (PEG-4000)
PH range: 5.4 - 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→52.6 Å / Num. obs: 29455 / % possible obs: 100 % / Redundancy: 6.92 % / Biso Wilson estimate: 76.042 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0451 / Rsym value: 0.027 / Net I/σ(I): 19
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6.67 % / Rmerge(I) obs: 0.5176 / Num. unique obs: 3375 / CC1/2: 0.901 / Rsym value: 0.402 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→52.59 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.244
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23626 1544 5.2 %RANDOM
Rwork0.2063 ---
obs0.20784 27910 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-1.68 Å2
2---1.02 Å2-0 Å2
3---2.2 Å2
Refinement stepCycle: 1 / Resolution: 2.4→52.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 54 210 4970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134859
X-RAY DIFFRACTIONr_bond_other_d0.0350.0154567
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.6446616
X-RAY DIFFRACTIONr_angle_other_deg2.2251.57310514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3865607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58721.66253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91615789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8291537
X-RAY DIFFRACTIONr_chiral_restr0.0590.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025478
X-RAY DIFFRACTIONr_gen_planes_other0.0240.021100
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0957.6012431
X-RAY DIFFRACTIONr_mcbond_other5.0967.5992430
X-RAY DIFFRACTIONr_mcangle_it7.0911.4183037
X-RAY DIFFRACTIONr_mcangle_other7.08911.423038
X-RAY DIFFRACTIONr_scbond_it5.1667.7822428
X-RAY DIFFRACTIONr_scbond_other5.1127.772413
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.00611.5263554
X-RAY DIFFRACTIONr_long_range_B_refined9.36888.9115180
X-RAY DIFFRACTIONr_long_range_B_other9.36388.8675168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 113 -
Rwork0.328 2047 -
obs--99.68 %

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