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- PDB-4r7p: Human UDP-glucose pyrophosphorylase isoform 1 in complex with UDP... -

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Basic information

Entry
Database: PDB / ID: 4r7p
TitleHuman UDP-glucose pyrophosphorylase isoform 1 in complex with UDP-glucose
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / Rossmann-like alpha/beta/alpha sandwich fold / pyrophosphorylase / UTP / Glc-1-P
Function / homology
Function and homology information


glucose 1-phosphate metabolic process / pyrimidine ribonucleotide binding / Formation of the active cofactor, UDP-glucuronate / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / D-glucose binding / glycogen biosynthetic process / glycogen metabolic process / Glycogen synthesis ...glucose 1-phosphate metabolic process / pyrimidine ribonucleotide binding / Formation of the active cofactor, UDP-glucuronate / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / D-glucose binding / glycogen biosynthetic process / glycogen metabolic process / Glycogen synthesis / brain development / extracellular exosome / identical protein binding / nucleus / metal ion binding / 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
ACETATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsFuehring, J. / Cramer, J.T. / Schneider, J. / Baruch, P. / Gerardy-Schahn, R. / Fedorov, R.
CitationJournal: Sci Rep
Title: A Quaternary Mechanism Enables the Complex Biological Functions of Octameric Human UDP-glucose Pyrophosphorylase, a Key Enzyme in Cell Metabolism.
Authors: Fuhring, J.I. / Cramer, J.T. / Schneider, J. / Baruch, P. / Gerardy-Schahn, R. / Fedorov, R.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
C: UTP--glucose-1-phosphate uridylyltransferase
D: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,45446
Polymers235,8094
Non-polymers3,64642
Water2,108117
1
A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
C: UTP--glucose-1-phosphate uridylyltransferase
D: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
C: UTP--glucose-1-phosphate uridylyltransferase
D: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,90992
Polymers471,6188
Non-polymers7,29184
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area31190 Å2
ΔGint-913 kcal/mol
Surface area177790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.970, 138.970, 311.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-610-

ZN

DetailsTwo cyclic C4 tetramers are stacked onto each other and are related by twofold symmetry axes creating the octameric structure with dihedral symmetry D4

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 58952.199 Da / Num. of mol.: 4 / Fragment: UDP-Glucose pyrophosphorylase / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGP2, UGP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q16851, UTP-glucose-1-phosphate uridylyltransferase

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Non-polymers , 6 types, 159 molecules

#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3.68 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 281.15 K / pH: 7.5
Details: The protein sample contained 10.3 mg/ml of hUGP, 50 mM HEPES pH 7.5, 5 mM MgCl2, 1 mM EDTA, 20% (w/v) sucrose and 4 mM UDP-Glc. 1 l of the hUGP UDP-Glc complex was mixed 1:1 with the ...Details: The protein sample contained 10.3 mg/ml of hUGP, 50 mM HEPES pH 7.5, 5 mM MgCl2, 1 mM EDTA, 20% (w/v) sucrose and 4 mM UDP-Glc. 1 l of the hUGP UDP-Glc complex was mixed 1:1 with the reservoir solution containing 100 mM sodium acetate buffer pH 4.8, 520 mM zinc acetate, 6% (w/v) aminocaproic acid and 75 mM ammonium sulfate. , VAPOR DIFFUSION, SITTING DROP, temperature 281.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2011
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.3→47.623 Å / Num. obs: 58213 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 12.3 % / Biso Wilson estimate: 96.27 Å2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→47.62 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 24.49 / Stereochemistry target values: ML
Details: Author stated the following: In the crystals of hUGP1-UDP-Glc complex the electron density for the substrate (UPG) as well as for some other parts of the structure was observed to be rather ...Details: Author stated the following: In the crystals of hUGP1-UDP-Glc complex the electron density for the substrate (UPG) as well as for some other parts of the structure was observed to be rather weak. It may in part be explained by a certain degree of disorder within the unit cell, which is reflected in a high value of the Wilson B-factor (108.6 A**2) and a weaker electron density for the protein chain D. However, the partial electron density observed for the UPG ribose and the glucose moieties indicated that the substrate is present in the active site of protein chain A. To improve the quality of the electron density, especially in its weak regions, we performed a phase improvement procedure using the density modification (DM) methods in the following way. The DM was performed in a solvent flattening mode using Hendrickson-Lattman coefficients from the refined protein model with omitted substrate and ligands as an initial approximation. After several cycles of the DM, we observed a noticeable increase of the figure-of-merit (15% in a high-resolution shell). The resulting weighted structure factor and modified phases from DM procedure were used to calculate the composite 2Fo-Fc electron density which you can see on the figure attached to this message. The DM-improved ligand-omit map allowed to determine the binding mode of UPG unambiguously. In addition to the UPG, the DM map allowed to resolve several other weak density regions which were not clearly interpretable before. The described method of improvement of the weak electron density regions has been successfully applied to resolve the disordered protein regions in a publication: Fedorov R, Witte G, Urbanke C, Manstein DJ, Curth U. 3D structure of Thermus aquaticus single-stranded DNA-binding protein gives insight into the functioning of SSB proteins. (2006) Nucleic Acids Res 34, 6708-6717. and in a number of application notes of our group together with Bruker company. The considerable increase of the electron density quality and the value of figure-of-merit in the particular case of hUGP1.UDP-Glc complex structure can be explained by a high solvent content in the hUGP1.UDP-Glc complex crystals (Vs = 67.7%), which makes the phase improvement by solvent flattening procedure very efficient.
RfactorNum. reflection% reflection
Rfree0.247 2580 5.06 %
Rwork0.199 --
obs0.202 50946 99.9 %
all-49306 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15292 0 182 117 15591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815718
X-RAY DIFFRACTIONf_angle_d1.10121248
X-RAY DIFFRACTIONf_dihedral_angle_d16.3485912
X-RAY DIFFRACTIONf_chiral_restr0.0422428
X-RAY DIFFRACTIONf_plane_restr0.0062714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.41440.34151400.28042637X-RAY DIFFRACTION100
3.4144-3.48410.30871350.26712666X-RAY DIFFRACTION100
3.4841-3.55980.29911590.22992643X-RAY DIFFRACTION100
3.5598-3.64260.29061410.21792656X-RAY DIFFRACTION100
3.6426-3.73370.26561590.21352612X-RAY DIFFRACTION100
3.7337-3.83460.22841240.20762672X-RAY DIFFRACTION100
3.8346-3.94740.25411300.18482683X-RAY DIFFRACTION100
3.9474-4.07470.27991360.17062660X-RAY DIFFRACTION100
4.0747-4.22020.20671630.17062652X-RAY DIFFRACTION100
4.2202-4.38910.2261610.14862630X-RAY DIFFRACTION100
4.3891-4.58870.21811400.152689X-RAY DIFFRACTION100
4.5887-4.83040.20561380.15242676X-RAY DIFFRACTION100
4.8304-5.13270.20691450.15422699X-RAY DIFFRACTION100
5.1327-5.52850.2321480.17062687X-RAY DIFFRACTION100
5.5285-6.08380.22531250.19032726X-RAY DIFFRACTION100
6.0838-6.96180.36481360.2432751X-RAY DIFFRACTION100
6.9618-8.76220.2491670.23042740X-RAY DIFFRACTION100
8.7622-47.62790.2331330.22952887X-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)
11.43360.6327-0.53282.4501-0.20412.21420.26060.18590.2441-0.1454-0.1926-0.317-0.29380.42860.03851.30170.61930.17731.00950.15050.408929.9816-23.014331.0992
21.1396-0.3653-0.28371.79290.51031.72560.13610.40330.0333-0.6717-0.2727-0.107-0.0632-0.14290.19791.53820.61630.2381.01130.19030.627563.2993-93.94827.7658
32.303-0.51240.02291.6239-0.08274.18150.10140.7922-0.0165-0.3951-0.11940.3102-0.3792-1.00610.09421.19440.4488-0.0141.1929-0.12770.68514.6736-76.7411.318
44.2572-0.4473-1.09491.8734-0.36272.91190.04370.31990.5942-0.4008-0.2299-0.9655-0.18781.17570.18451.37520.19340.25151.14180.3121.108378.5088-40.177647.6058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 24 through 508)
2X-RAY DIFFRACTION2(chain 'B' and resid 24 through 508)
3X-RAY DIFFRACTION3(chain 'C' and resid 24 through 508)
4X-RAY DIFFRACTION4(chain 'D' and resid 24 through 508)

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