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- PDB-3r2w: Crystal Structure of UDP-glucose Pyrophosphorylase of Homo Sapiens -

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Basic information

Entry
Database: PDB / ID: 3r2w
TitleCrystal Structure of UDP-glucose Pyrophosphorylase of Homo Sapiens
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / Homo sapiens / Rossmann Fold Beta Barrel / Nucleotidyltransferase
Function / homology
Function and homology information


pyrimidine ribonucleotide binding / glucose 1-phosphate metabolic process / Formation of the active cofactor, UDP-glucuronate / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / D-glucose binding / glycogen biosynthetic process / glycogen metabolic process / Glycogen synthesis ...pyrimidine ribonucleotide binding / glucose 1-phosphate metabolic process / Formation of the active cofactor, UDP-glucuronate / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-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 / 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
UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.6 Å
AuthorsZheng, X. / Yu, Q.
CitationJournal: Biochem.J. / Year: 2012
Title: The crystal structure of human UDP-glucose pyrophosphorylase reveals a latch effect that influences enzymatic activity.
Authors: Yu, Q. / Zheng, X.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Sep 9, 2020Group: Database references / Structure summary / Category: struct / struct_ref_seq_dif / Item: _struct.title / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)236,7384
Polymers236,7384
Non-polymers00
Water00
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

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


Theoretical massNumber of molelcules
Total (without water)473,4758
Polymers473,4758
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area17850 Å2
ΔGint-72 kcal/mol
Surface area169340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.445, 140.445, 311.724
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 59184.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGP2, UGP1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: Q16851, UTP-glucose-1-phosphate uridylyltransferase

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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: 3.75 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MgSO4, 35.8% PEG3350, glycerol, HEPES, pH 6.5, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 15, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→120 Å / Num. all: 39283 / Num. obs: 39283 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.6→3.69 Å / % possible all: 64.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.6→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.891 / Occupancy max: 1 / Occupancy min: 1 / SU B: 79.886 / SU ML: 0.542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.695 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3038 1985 5.1 %RANDOM
Rwork0.2475 37298 --
obs0.2502 39283 93.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 119.77 Å2 / Biso mean: 144.356 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-4.72 Å22.36 Å20 Å2
2--4.72 Å20 Å2
3----7.08 Å2
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13938 0 0 0 13938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02214181
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.96819301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03251837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34124.828582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.049152291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9291564
X-RAY DIFFRACTIONr_chiral_restr0.10.22318
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110601
X-RAY DIFFRACTIONr_mcbond_it0.4681.59193
X-RAY DIFFRACTIONr_mcangle_it0.9214783
X-RAY DIFFRACTIONr_scbond_it1.07134988
X-RAY DIFFRACTIONr_scangle_it1.9464.54518
LS refinement shellResolution: 3.6→3.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 80 -
Rwork0.368 1558 -
all-1638 -
obs--55.19 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.7885-0.38320.15930.88530.33760.538-0.0468-0.2370.1080.32780.06640.2411-0.1427-0.374-0.01950.90060.1432-0.01011.1487-0.05691.0677-75.960224.92232.2724
24.3669-0.24370.84822.23980.86394.0348-0.3383-0.1448-0.06150.36680.3074-0.13390.1639-0.25120.03090.54620.1413-0.12580.8005-0.01440.4996-55.591720.4421-4.1011
30.19930.661-0.518238.6744-32.147626.7359-0.18370.2414-0.80793.05660.2365-0.1704-2.6003-0.2647-0.05280.9053-0.59920.53781.6321-0.67263.5629-81.07013.6834-1.0702
44.1062.4855-0.82645.8281-1.78634.1794-0.0367-0.37110.54770.39160.03830.1624-0.5577-0.8536-0.00160.46650.3063-0.14380.8252-0.11520.737-63.599528.94730.7872
52.5188-1.1299-2.03411.726-1.64277.38250.15440.40550.47720.04050.1559-0.0387-0.1468-0.8039-0.31030.71920.3283-0.12920.8842-0.00771.0278-74.084238.3612-8.5678
62.38341.34240.45142.8179-1.09751.1296-0.2368-0.12980.059-0.30260.28320.3951-0.0471-0.6485-0.04640.71410.3123-0.13191.1427-0.11710.9361-76.741629.6251-6.3441
76.72270.2583-0.12151.13181.0935.21240.03130.13290.31720.1351-0.1211-0.3107-0.59010.10460.08980.41550.0593-0.17290.8455-0.0080.4484-56.468523.1425-25.6704
85.1489-1.53473.87794.932.91886.7385-0.2842-0.21420.45340.09640.0431-0.465-0.1729-0.17520.24110.33540.0133-0.00920.82740.01310.4448-56.612919.777-36.3942
912.67622.03982.55753.6199-2.09244.29540.04330.4737-0.5161-0.22230.0631-0.43140.39910.0712-0.10640.39580.08080.08720.7804-0.12230.6316-55.123312.7857-41.0361
108.2687-7.311.805816.8053-0.80251.556-0.3707-0.0053-0.2040.69120.0992-0.22590.2004-0.10110.27140.48220.01790.09620.6823-0.00490.5681-54.219810.2505-43.6731
114.67640.4540.7914.98711.79852.5653-0.17380.0560.0352-0.53750.2844-0.0655-0.1102-0.3232-0.11060.8746-0.1382-0.04771.36210.03140.7879-32.08230.1865-102.2818
122.5654-0.12850.24442.9549-0.33812.05020.03160.03720.2271-0.05070.0268-0.1302-0.0344-0.0271-0.05850.2233-0.0829-0.00020.90060.13310.6446-20.295716.2033-73.1976
136.93912.71132.62354.13441.81352.1909-0.22340.481-0.2059-0.38920.1841-0.0212-0.1577-0.01660.03920.6261-0.02470.00720.95360.20240.4893-27.303615.172-88.4027
143.72232.3571-0.55513.8135-1.10583.30140.07080.0905-0.1431-0.2145-0.0107-0.0574-0.00790.1669-0.06010.1436-0.03940.0030.98760.03510.646-12.387711.0079-73.6235
150.99410.05861.05552.36830.35781.52150.17640.1656-0.4782-0.4059-0.03950.47160.58430.0898-0.13690.6487-0.06770.15651.06440.02941.0345-20.7452-3.4121-78.2479
163.0048-2.64191.41723.51940.40713.21830.26320.1799-0.2885-0.2590.02910.0760.267-0.0833-0.29230.3182-0.19590.08451.04450.25970.725-24.94421.6924-80.0525
175.9009-0.1473-0.78695.05340.58263.7347-0.1936-0.202-0.07420.2878-0.0165-0.1492-0.2530.25250.21020.2426-0.0136-0.00550.82820.13090.6386-35.245314.2296-59.1529
185.85710.38790.68397.26311.8767.2526-0.32640.02210.381-0.39730.0852-0.01150.1956-0.04850.24130.24810.01090.15010.73940.13630.5219-45.783310.5363-51.9011
1910.91684.96548.25672.26043.76176.268-0.240.31380.4127-0.07650.03120.1648-0.14120.07520.20880.5020.08570.14121.15570.13750.98-43.291913.3618-44.091
209.3857-9.35210.39529.45670.09134.33130.41010.72650.4651-0.6362-0.5654-0.499-0.34230.47680.15530.4922-0.12170.05050.720.03350.7944-56.2213.9174-48.8632
210.91972.5550.00597.16920.01680.0029-0.2809-0.02970.1353-0.5610.21940.4044-0.00910.00680.06151.59210.06690.06912.07330.05551.6108-52.724556.8263-80.5816
221.680.55610.5891.11670.10161.0186-0.0511-0.19010.5012-0.19330.2014-0.2289-0.68780.0175-0.15041.03830.0026-0.01940.98010.15981.2388-70.916754.3741-53.0073
230.23650.27270.52361.87171.13872.1320.10340.20720.2525-0.3917-0.3057-0.259-0.2893-0.24770.20231.19830.1307-0.00751.05660.31591.2938-73.595953.3587-65.7439
246.49070.8380.5570.2150.15590.15570.07470.5980.5484-0.14580.0465-0.2706-0.33180.0969-0.12111.4415-0.0032-0.031.21960.19461.3679-67.858560.6219-59.7831
250.74821.6420.27934.06330.39072.30750.1431-0.10890.0485-0.2715-0.3405-0.2222-0.73480.31780.19741.3093-0.0220.06121.0344-0.03531.3451-64.868457.7776-42.6365
261.65810.5644-1.09730.9120.07421.22210.1729-0.08570.0146-0.2077-0.0999-0.0166-0.07280.439-0.0731.1468-0.0435-0.09741.11720.05121.4261-54.681152.4977-52.7675
270.32810.0352-0.20463.8080.09470.23220.4523-0.21270.33460.439-0.4828-0.0019-0.5230.13250.03051.3316-0.204-0.09531.06580.07010.9687-73.134246.2586-43.5024
282.85560.5367-1.34949.0797-1.17663.5708-0.15580.24960.4676-0.18960.265-0.0391-0.0429-0.2192-0.10920.2686-0.0024-0.09790.78690.02940.6864-76.246925.8903-47.0172
2915.74930.3864-2.52960.36820.36861.77730.2660.12120.1537-0.3789-0.2592-0.2734-0.6032-0.4262-0.00680.57390.03940.11880.81310.1540.8575-78.722815.6434-48.115
309.52464.50573.44067.25386.21335.3552-0.1743-0.007-0.1931-0.04120.14890.01-0.03780.07020.02540.51230.0119-0.01350.57920.18430.7377-79.545513.259-46.4036
314.425-0.27491.43823.23340.43958.07380.0270.3818-0.5406-0.25130.15930.24321.1019-0.0181-0.18630.7370.13730.02910.99070.16950.7782-102.3758-41.9469-23.6493
324.031-0.27720.53681.70720.49852.1924-0.0981-0.31320.1549-0.14560.02140.19490.018-0.11660.07660.27160.00770.0760.82550.20780.5487-113.9598-9.2593-30.1108
333.4968-1.12370.44554.48181.04241.01570.1402-0.13980.31410.0963-0.0419-0.57310.25030.0821-0.09830.37130.10550.01890.95190.25730.4927-106.3096-16.2984-19.0418
341.3227-0.6740.25371.59410.5081.1342-0.1933-0.0253-0.14950.2918-0.10480.38610.2535-0.0890.29810.29840.03420.10080.97090.23810.5854-117.5667-17.4292-27.2424
354.1677-4.3632-1.60964.72021.79821.02760.24810.3231-0.1468-0.351-0.1641-0.14670.39060.1174-0.08411.0434-0.05770.23991.20520.06920.792-111.193-23.3611-48.5211
363.0856-2.05872.22173.1296-0.2922.4660.18870.4595-0.0521-0.0315-0.1113-0.10890.33880.345-0.07740.44340.02580.17460.99660.17310.5855-109.9487-26.2154-33.2391
373.13542.10920.18943.41680.64271.1-0.0463-0.06370.27-0.14480.12360.2408-0.0316-0.1748-0.07730.32730.0428-0.02120.89390.18020.4849-104.0716-3.021-36.5677
387.1113-1.7121-0.68535.72960.15875.6739-0.22-0.14320.49460.0660.2112-0.3610.102-0.11410.00880.2412-0.09050.05730.69760.11570.5086-88.83235.8732-41.9922
393.6474-2.7606-2.55227.84771.79431.8036-0.21220.1423-0.1546-0.86230.04350.23640.092-0.09150.16870.7113-0.0648-0.14020.79750.1840.8098-89.197413.4328-44.043
407.57641.0238-0.62122.96440.53880.19390.0486-0.1682-0.36250.1715-0.0052-0.31220.08020-0.04350.50440.02190.05110.60590.09440.7663-77.8479.9675-42.0059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 106
2X-RAY DIFFRACTION2A107 - 193
3X-RAY DIFFRACTION3A207 - 210
4X-RAY DIFFRACTION4A218 - 266
5X-RAY DIFFRACTION5A267 - 308
6X-RAY DIFFRACTION6A309 - 391
7X-RAY DIFFRACTION7A392 - 448
8X-RAY DIFFRACTION8A449 - 481
9X-RAY DIFFRACTION9A482 - 495
10X-RAY DIFFRACTION10A496 - 497
11X-RAY DIFFRACTION11B18 - 67
12X-RAY DIFFRACTION12B76 - 169
13X-RAY DIFFRACTION13B170 - 241
14X-RAY DIFFRACTION14B242 - 286
15X-RAY DIFFRACTION15B287 - 357
16X-RAY DIFFRACTION16B358 - 391
17X-RAY DIFFRACTION17B392 - 451
18X-RAY DIFFRACTION18B452 - 489
19X-RAY DIFFRACTION19B490 - 496
20X-RAY DIFFRACTION20B497 - 498
21X-RAY DIFFRACTION21C26 - 50
22X-RAY DIFFRACTION22C51 - 153
23X-RAY DIFFRACTION23C154 - 189
24X-RAY DIFFRACTION24C219 - 254
25X-RAY DIFFRACTION25C255 - 299
26X-RAY DIFFRACTION26C300 - 373
27X-RAY DIFFRACTION27C374 - 424
28X-RAY DIFFRACTION28C425 - 481
29X-RAY DIFFRACTION29C482 - 494
30X-RAY DIFFRACTION30C495 - 497
31X-RAY DIFFRACTION31D22 - 68
32X-RAY DIFFRACTION32D76 - 144
33X-RAY DIFFRACTION33D145 - 193
34X-RAY DIFFRACTION34D216 - 285
35X-RAY DIFFRACTION35D286 - 322
36X-RAY DIFFRACTION36D323 - 376
37X-RAY DIFFRACTION37D377 - 445
38X-RAY DIFFRACTION38D446 - 487
39X-RAY DIFFRACTION39D488 - 496
40X-RAY DIFFRACTION40D497 - 498

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