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- PDB-7ljs: Porcine Dihydropyrimidine dehydrogenase (DPD) complexed with 5-Et... -

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Basic information

Entry
Database: PDB / ID: 7ljs
TitlePorcine Dihydropyrimidine dehydrogenase (DPD) complexed with 5-Ethynyluracil (5EU) - Open Form
ComponentsDihydropyrimidine dehydrogenase [NADP(+)]
KeywordsFLAVOPROTEIN / Dihydropyrimidine dehydrogenase / DPD / dehydrogenase / 5-Ethynyluracil / 5EU / inhibitor / inactivator
Function / homology
Function and homology information


dihydropyrimidine dehydrogenase (NADP+) / uracil binding / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / beta-alanine biosynthetic process / uracil catabolic process / thymine catabolic process / FMN binding / NADP binding / flavin adenine dinucleotide binding ...dihydropyrimidine dehydrogenase (NADP+) / uracil binding / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / beta-alanine biosynthetic process / uracil catabolic process / thymine catabolic process / FMN binding / NADP binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / 4Fe-4S dicluster domain / Alpha-helical ferredoxin / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. ...Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / 4Fe-4S dicluster domain / Alpha-helical ferredoxin / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / 5-ethynylpyrimidine-2,4(1H,3H)-dione / Dihydropyrimidine dehydrogenase [NADP(+)]
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsButrin, A. / Forouzesh, D. / Beaupre, B. / Wawrzak, Z. / Liu, D. / Moran, G.
CitationJournal: Biochemistry / Year: 2021
Title: The Interaction of Porcine Dihydropyrimidine Dehydrogenase with the Chemotherapy Sensitizer: 5-Ethynyluracil.
Authors: Forouzesh, D.C. / Beaupre, B.A. / Butrin, A. / Wawrzak, Z. / Liu, D. / Moran, G.R.
History
DepositionJan 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
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: Dihydropyrimidine dehydrogenase [NADP(+)]
B: Dihydropyrimidine dehydrogenase [NADP(+)]
C: Dihydropyrimidine dehydrogenase [NADP(+)]
D: Dihydropyrimidine dehydrogenase [NADP(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,55232
Polymers446,4134
Non-polymers11,13828
Water39,1112171
1
A: Dihydropyrimidine dehydrogenase [NADP(+)]
B: Dihydropyrimidine dehydrogenase [NADP(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,77616
Polymers223,2072
Non-polymers5,56914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30350 Å2
ΔGint-284 kcal/mol
Surface area68810 Å2
MethodPISA
2
C: Dihydropyrimidine dehydrogenase [NADP(+)]
D: Dihydropyrimidine dehydrogenase [NADP(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,77616
Polymers223,2072
Non-polymers5,56914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30240 Å2
ΔGint-281 kcal/mol
Surface area69800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.031, 160.046, 164.074
Angle α, β, γ (deg.)90.000, 95.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydropyrimidine dehydrogenase [NADP(+)] / DPD / Dihydrothymine dehydrogenase / Dihydrouracil dehydrogenase


Mass: 111603.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DPYD / Production host: Escherichia coli (E. coli)
References: UniProt: Q28943, dihydropyrimidine dehydrogenase (NADP+)

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Non-polymers , 5 types, 2199 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Chemical
ChemComp-Y3G / 5-ethynylpyrimidine-2,4(1H,3H)-dione


Mass: 136.108 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2171 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Drops were formed by mixing 3 uL of 39 uM of DPD, 1 mM 5EU, 1 mM NADPH in 25 mM HEPES, 10 mM DTT, 10% glycerol pH 7.5 with 3 uL of well solution (1 mL) containing 50-200 mM NaCl, 19% PEG 6000, 1 mM DTT pH 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.127 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 255614 / % possible obs: 90.2 % / Redundancy: 2.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.121 / Rrim(I) all: 0.211 / Net I/σ(I): 5.6
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9241 / CC1/2: 0.377 / Rpim(I) all: 0.665 / % possible all: 66

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H7X

1h7x


Resolution: 2→45.62 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 10691 4.88 %
Rwork0.1721 208462 -
obs0.1749 219153 77.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.14 Å2 / Biso mean: 30.5255 Å2 / Biso min: 13.98 Å2
Refinement stepCycle: final / Resolution: 2→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30769 0 504 2171 33444
Biso mean--22.72 37.5 -
Num. residues----4033
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.31861340.22872797293131
2.02-2.040.2941700.2253416358638
2.04-2.070.32142100.2184088429846
2.07-2.090.28132280.22564611483951
2.09-2.120.29472550.22195116537157
2.12-2.150.25642830.20745378566160
2.15-2.180.28572930.20415667596063
2.18-2.210.25153020.19535725602763
2.21-2.250.29673320.18755856618865
2.25-2.290.27082850.18955884616965
2.29-2.330.2712770.19055989626666
2.33-2.370.26023260.20045997632367
2.37-2.410.24333330.20076165649868
2.41-2.460.26492950.19126369666471
2.46-2.520.27093210.19356542686373
2.52-2.570.27532990.19266917721676
2.57-2.640.25883900.20477274766481
2.64-2.710.24813930.20788123851690
2.71-2.790.25244230.19888663908696
2.79-2.880.2684320.20078792922497
2.88-2.980.26714500.19118850930098
2.98-3.10.25715000.19238804930498
3.1-3.240.22865280.18038816934499
3.24-3.410.22064750.1738895937098
3.41-3.630.22354510.1678893934499
3.63-3.910.20834220.15448967938998
3.91-4.30.19684670.14398884935199
4.3-4.920.18364690.13558882935199
4.92-6.20.21164940.15239011950599
6.2-45.620.17724540.14369091954599
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)
10.7563-0.03530.38420.5152-0.07180.1212-0.0472-0.07730.01410.09280.0309-0.0151-0.03210.06830.00070.2741-0.0137-0.00460.28560.03360.231194.2365.624280.1748
20.4413-0.1733-0.29650.59030.31380.43910.02540.09160.0103-0.007-0.03790.0515-0.0511-0.0434-0.00590.2026-0.004-0.00930.20740.00720.217356.424672.715279.1162
31.1348-0.12580.69290.20050.19960.9874-0.0151-0.1032-0.03440.06750.0351-0.02160.0112-0.0063-0.00350.28160.00940.02420.27630.00050.252460.864180.3386102.0456
40.2361-0.0649-0.06340.47610.25610.59020.00430.0188-0.0531-0.022-0.03120.07860.0723-0.03720.00190.1893-0.0276-0.01120.25150.00250.240951.624852.703458.1052
50.5982-0.10170.06480.1792-0.29130.55650.01950.0648-0.0016-0.0246-0.0066-0.0139-0.00530.0393-0.00950.2126-0.01960.00090.25530.01510.213968.370956.050651.3286
60.9164-0.13340.1730.1353-0.01770.48360.04390.08880.2065-0.09620.013-0.0324-0.24210.03220.0050.338-0.01170.00930.2910.05130.299187.91474.237163.1411
70.6761-0.0004-0.25320.3142-0.16250.2032-0.0233-0.10610.04460.06610.03940.0745-0.0013-0.0382-0.00610.2601-0.01530.02140.3039-0.0050.273861.295351.051984.7477
80.8236-0.07860.22390.2014-0.09550.82380.0132-0.0803-0.07980.04470.0245-0.02440.07880.1109-0.00050.22980.0054-0.00040.23560.0080.2168100.459543.090393.4068
90.9968-0.0706-0.03370.87830.17171.1576-0.0368-0.0002-0.14210.091-0.02550.0150.13170.02730.00120.28540.05660.00260.39410.03030.211284.188648.4499110.7623
100.6929-0.6235-0.14730.45060.11140.5538-0.0109-0.03640.2378-0.01430.0174-0.0741-0.13450.0026-0.00030.3911-0.012-0.01750.39480.00950.294690.208659.4708116.0584
110.23990.00040.15850.224-0.20770.8673-0.00640.02490.01840.02830.0224-0.0002-0.09950.120.0120.1996-0.00740.00990.2052-0.00440.2046104.948550.531469.0755
120.58330.3267-0.02330.69960.20031.03830.03590.22320.1519-0.27020.01530.0973-0.0592-0.0259-0.00340.28730.01430.01150.3342-0.00430.242899.341846.348536.7523
130.4439-0.32150.42340.6669-0.09680.49090.0225-0.0041-0.0380.02840.06050.07760.0101-0.0478-0.00640.2184-0.01290.00880.2731-0.00090.226187.873943.627255.5822
140.5996-0.0595-0.2540.19370.19980.0929-0.0414-0.1695-0.23020.12310.01560.06570.1996-0.0291-0.01330.3078-0.01820.01270.23490.03180.290567.204634.656776.5266
150.85550.0668-0.14940.1027-0.04030.38260.0050.06440.03-0.01280.00510.0059-0.0105-0.00990.00350.18980.0061-0.00590.164-0.00150.187160.66295.3249-9.3114
160.24190.09010.11690.10050.13380.8021-0.01720.0981-0.02-0.04750.00650.00330.0725-0.00750.00330.2263-0.00170.00950.2286-0.00650.216372.526891.5591-22.3337
170.68010.14290.09810.39680.16750.09470.018-0.10040.02520.0553-0.0109-0.005-0.003-0.03170.00990.1862-0.00160.00970.205-0.01460.189965.090998.174124.2098
180.65840.05790.28890.35060.09520.3061-0.03030.13780.0962-0.09650.03140.0095-0.12640.0663-0.00110.24330.00220.00230.17170.00880.230643.0273108.60720.5063
190.90320.14160.18310.24430.06930.24730.0593-0.0271-0.05090.0059-0.0361-0.00120.030.0308-0.00080.19040.00630.00520.1625-0.00860.185847.296175.09620.5479
201.34380.078-0.75610.19170.22310.9681-0.00080.1345-0.0432-0.06790.00330.01540.011-0.0285-0.01240.24-0.0033-0.01560.2158-0.01270.233132.958561.1492-18.9982
210.731-0.0896-0.10050.1940.00490.33480.0026-0.0686-0.06280.045-0.0077-0.00280.0555-0.0059-0.00180.195-0.019-0.01080.19790.00870.182444.190185.358622.9508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 78 )A2 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 237 )A79 - 237
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 488 )A238 - 488
4X-RAY DIFFRACTION4chain 'A' and (resid 489 through 660 )A489 - 660
5X-RAY DIFFRACTION5chain 'A' and (resid 661 through 879 )A661 - 879
6X-RAY DIFFRACTION6chain 'A' and (resid 880 through 1017 )A880 - 1017
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 78 )B3 - 78
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 302 )B79 - 302
9X-RAY DIFFRACTION9chain 'B' and (resid 303 through 373 )B303 - 373
10X-RAY DIFFRACTION10chain 'B' and (resid 374 through 461 )B374 - 461
11X-RAY DIFFRACTION11chain 'B' and (resid 462 through 631 )B462 - 631
12X-RAY DIFFRACTION12chain 'B' and (resid 632 through 701 )B632 - 701
13X-RAY DIFFRACTION13chain 'B' and (resid 702 through 861 )B702 - 861
14X-RAY DIFFRACTION14chain 'B' and (resid 862 through 1018 )B862 - 1018
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 237 )C2 - 237
16X-RAY DIFFRACTION16chain 'C' and (resid 238 through 581 )C238 - 581
17X-RAY DIFFRACTION17chain 'C' and (resid 582 through 879 )C582 - 879
18X-RAY DIFFRACTION18chain 'C' and (resid 880 through 1017 )C880 - 1017
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 196 )D2 - 196
20X-RAY DIFFRACTION20chain 'D' and (resid 197 through 511 )D197 - 511
21X-RAY DIFFRACTION21chain 'D' and (resid 512 through 1019 )D512 - 1019

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