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- PDB-8f6n: Dihydropyrimidine Dehydrogenase (DPD) C671S Mutant Soaked with Th... -

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Basic information

Entry
Database: PDB / ID: 8f6n
TitleDihydropyrimidine Dehydrogenase (DPD) C671S Mutant Soaked with Thymine Quasi-Anaerobically
ComponentsDihydropyrimidine dehydrogenase [NADP(+)]
KeywordsFLAVOPROTEIN / dihydropyrimidine dehydrogenase / dehydrogenase / mutant / thymine
Function / homology
Function and homology information


dihydropyrimidine dehydrogenase (NADP+) / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / uracil binding / beta-alanine biosynthetic process / thymine catabolic process / uracil catabolic process / FMN binding / NADP binding / flavin adenine dinucleotide binding ...dihydropyrimidine dehydrogenase (NADP+) / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / uracil binding / beta-alanine biosynthetic process / thymine catabolic process / uracil 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 / THYMINE / Dihydropyrimidine dehydrogenase [NADP(+)]
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsKaley, N. / Smith, M. / Forouzesh, D. / Liu, D. / Moran, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1904480 United States
National Science Foundation (NSF, United States)2203593 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2023
Title: Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes.
Authors: Smith, M.M. / Forouzesh, D.C. / Kaley, N.E. / Liu, D. / Moran, G.R.
History
DepositionNov 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)457,44732
Polymers446,3494
Non-polymers11,09828
Water10,683593
1
A: Dihydropyrimidine dehydrogenase [NADP(+)]
B: Dihydropyrimidine dehydrogenase [NADP(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,72416
Polymers223,1752
Non-polymers5,54914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31060 Å2
ΔGint-276 kcal/mol
Surface area68630 Å2
MethodPISA
2
C: Dihydropyrimidine dehydrogenase [NADP(+)]
D: Dihydropyrimidine dehydrogenase [NADP(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,72416
Polymers223,1752
Non-polymers5,54914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30760 Å2
ΔGint-277 kcal/mol
Surface area67920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.445, 158.144, 165.707
Angle α, β, γ (deg.)90.00, 96.78, 90.00
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(+)] / DHPDHase / DPD / Dihydrothymine dehydrogenase / Dihydrouracil dehydrogenase


Mass: 111587.281 Da / Num. of mol.: 4 / Mutation: C671S
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, 621 molecules

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


Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#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-TDR / THYMINE


Mass: 126.113 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 48.82 %
Description: Crystals grew as single elongated rectangular hexahedrons (200 x 50 x 50 uM).
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: DPD variant C671S (39.2 uM) in 25 mM HEPES, 2 mM DTT, 10% glycerol at pH 7.5 was mixed 1:1 with well solution containing 100 mM sodium citrate, 2 mM DTT, 19% PEG 6000 at pH 4.7 to yield a 6 ...Details: DPD variant C671S (39.2 uM) in 25 mM HEPES, 2 mM DTT, 10% glycerol at pH 7.5 was mixed 1:1 with well solution containing 100 mM sodium citrate, 2 mM DTT, 19% PEG 6000 at pH 4.7 to yield a 6 uL drop. Crystallization was carried out in the dark to prevent photo-degradation of the somewhat dissociable FMN cofactor. Under these conditions DPD crystals appeared within 16 hours and were left to grow for additional 24 hours. Ligands were combined with the crystals under near anaerobic conditions as follows: before being placed in a Plas-Labs 830 series glove box, the well solution beneath selected crystallization drops were made anaerobic with the addition of 10 mM dithionite and resealed with the cover slide. Crystals trays were placed in the glove box that contained a Motic binocular microscope coupled to an Accuscope 1080p high-definition camera. The glove box was sealed and made quasi-anaerobic by flushing with high-purity nitrogen gas for approximately 10 minutes at which time fractional dioxygen was recorded as 0.1 %, by a Forensics Detectors oxygen meter. Atmospheric dioxygen was measured throughout the soaking procedure and was held <1%. C671S DPD crystals were soaked for a minimum of 20 minutes with thymine (100 uM), each dissolved in the following cryo-solution: 20 mM sodium citrate, 0.4 mM DTT, 20% PEG 6000, 20% PEG 400, pH 7.5. The crystals were then submerged in liquid nitrogen, removed from the anaerobic environment, and stored under liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 2.12→114.022 Å / Num. obs: 146043 / % possible obs: 88 % / Redundancy: 4.9 % / Biso Wilson estimate: 29.82 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.091 / Rrim(I) all: 0.202 / Net I/σ(I): 7.3
Reflection shellResolution: 2.121→2.197 Å / Rmerge(I) obs: 1.175 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7307 / CC1/2: 0.433 / Rpim(I) all: 0.779 / Rrim(I) all: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7M31

7m31


Resolution: 2.12→26.98 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2442 7333 5.02 %
Rwork0.1824 --
obs0.1855 145954 61.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→26.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30952 0 0 593 31545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.038
X-RAY DIFFRACTIONf_angle_d2.67
X-RAY DIFFRACTIONf_dihedral_angle_d11.2654271
X-RAY DIFFRACTIONf_chiral_restr2.0184906
X-RAY DIFFRACTIONf_plane_restr0.0225463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.150.947320.240828X-RAY DIFFRACTION0
2.15-2.170.423820.2448101X-RAY DIFFRACTION1
2.17-2.20.248790.238280X-RAY DIFFRACTION4
2.2-2.220.3543280.244526X-RAY DIFFRACTION7
2.22-2.250.3155380.255838X-RAY DIFFRACTION11
2.25-2.280.3305720.26551380X-RAY DIFFRACTION18
2.29-2.320.34941040.272022X-RAY DIFFRACTION27
2.32-2.350.31571240.26412449X-RAY DIFFRACTION32
2.35-2.390.32321440.25332835X-RAY DIFFRACTION38
2.39-2.430.30371520.24883154X-RAY DIFFRACTION42
2.43-2.470.31821820.2423464X-RAY DIFFRACTION46
2.47-2.510.29832070.23943728X-RAY DIFFRACTION50
2.51-2.560.32382390.23614074X-RAY DIFFRACTION55
2.56-2.620.29972540.23614525X-RAY DIFFRACTION61
2.62-2.670.2892640.23465052X-RAY DIFFRACTION67
2.67-2.730.29722790.23595407X-RAY DIFFRACTION72
2.73-2.80.27223190.22525692X-RAY DIFFRACTION76
2.8-2.880.27453490.22816001X-RAY DIFFRACTION80
2.88-2.960.26613340.22266275X-RAY DIFFRACTION83
2.96-3.060.28523450.226609X-RAY DIFFRACTION88
3.06-3.170.28743910.21637061X-RAY DIFFRACTION94
3.17-3.290.26923590.20257290X-RAY DIFFRACTION97
3.29-3.440.2534090.18917511X-RAY DIFFRACTION100
3.44-3.620.25613910.18097483X-RAY DIFFRACTION100
3.63-3.850.23563810.16977522X-RAY DIFFRACTION100
3.85-4.150.22373980.15447521X-RAY DIFFRACTION99
4.15-4.560.20814070.13547402X-RAY DIFFRACTION98
4.56-5.220.2133530.14577419X-RAY DIFFRACTION98
5.22-6.560.21483980.15697334X-RAY DIFFRACTION97
6.56-26.980.17473990.14487638X-RAY DIFFRACTION100
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)
10.0442-0.02480.04530.0061-0.02060.0475-0.0384-0.0546-0.02160.0192-00.0296-0.07150.041900.18510.0199-0.03180.18190.02390.1814-20.983-19.2407-78.9655
20.1180.074-0.14920.0381-0.08790.1244-0.0011-0.04290.0245-0.0261-0.00790.0017-0.006-0.030200.1506-0.01560.00690.10.00540.138821.7936-11.1934-78.8662
30.10190.1126-0.08660.0844-0.08270.0955-0.0373-0.04380.0294-0.02920.02370.0106-0.0775-0.039600.1563-0.00640.01870.11010.00990.153531.31374.4249-91.6246
40.02640.03780.00980.05660.01110.00210.06080.00330.0859-0.0084-0.0168-0.05890.019-0.073700.1873-0.0053-0.02920.27970.03950.212110.9288-2.7734-102.5926
50.03570.2004-0.00320.0442-0.27090.0268-0.05340.0245-0.03020.00040.0126-0.07410.13790.00440.0070.2024-0.00440.04070.18360.01010.169830.9417-11.9784-88.1303
60.0815-0.001-0.14260.22860.06150.14930.0487-0.0436-0.0416-0.0093-0.04770.0077-0.01560.02240.00040.0901-0.0284-0.01970.11110.02220.090420.0544-30.3737-49.8068
70.1980.0719-0.07550.0221-0.02690.06650.1765-0.09480.11120.05350.06610.1044-0.01440.06010.10790.22830.05460.01690.0725-0.03180.27143.4665-0.2986-70.8612
80.0045-0.0221-0.0240.02840.04860.05180.10490.0734-0.01150.0685-0.05690.0794-0.07650.0731-0.00130.1826-0.0016-0.0090.1339-0.01260.1807-11.8603-11.0045-60.5491
90.05780.07320.03630.07650.09230.02870.02620.0689-0.1137-0.0182-0.02590.0074-0.04820.0008-00.14130.020.01670.1905-0.02120.172619.7327-29.36-84.5188
100.1731-0.09210.00460.091-0.0820.1810.02390.0594-0.01410.0344-0.0211-0.06160.0102-0.03880.00050.1010.0109-0.00320.1382-0.02260.0836-17.3839-38.1889-94.5312
110.0360.01130.04220.0318-0.0280.0781-0.1718-0.0022-0.09180.03690.0026-0.05490.07470.0138-0.00240.23040.02640.02430.37690.04160.15760.0243-29.7155-111.1206
120.0884-0.0256-0.0304-0.04420.03510.1440.0244-0.0024-0.00780.0089-0.02180.0166-0.0345-0.02290.00080.112-0.0114-0.00740.11890.01230.1085-14.1817-30.9383-67.3155
130.06940.0353-0.0722-0.00190.00050.0250.09780.057-0.2251-0.0518-0.0441-0.06130.0194-0.00220.02440.25050.03520.05080.0845-0.04970.20567.9648-48.8417-79.9965
140.08710.0089-0.02190.0341-0.04880.0727-0.00330.07810.0022-0.01070.0826-0.06460.17560.05110.00140.18160.00850.01960.07890.01430.224.2093-42.7684-71.5502
150.01750.00260.01750.01390.01450.01540.0514-0.03270.03940.0127-0.03230.00110.00160.001-00.2148-0.0143-0.010.15810.00650.188942.90499.96196.5921
160.12430.0196-0.02780.0013-0.02730.10910.003-0.08870.0022-0.04490.0197-0.0363-0.03-0.0459-00.1527-0.01810.00040.21160.01720.12195.680917.608917.594
170.01610.0109-0.01460.0291-0.04060.0431-0.0726-0.0460.08910.04750.0450.00040.0383-0.0476-0.00010.19410.0330.00730.24820.02770.161722.30569.670133.417
180.1673-0.0612-0.1408-0.06760.10470.2622-0.0527-0.0139-0.0658-0.0342-0.01470.03160.1364-0.0384-0.00950.1704-0.03980.01560.14410.03870.13715.56598.075716.4089
190.0986-0.00530.00870.1811-0.00030.1125-0.0030.06490.0235-0.0060.02240.02130.00630.0141-00.092-0.024-0.00260.18530.02590.104913.825215.9557-31.3325
200.241-0.0913-0.06150.0546-0.00750.02970.08270.06210.13210.0705-0.05530.01810.0182-0.02120.01660.1712-0.0408-0.00230.0931-0.00480.144426.625123.08333.9629
210.10260.02490.02950.07750.05840.10760.03040.0444-0.0212-0.046-0.011-0.0763-0.10510.10060.07540.1215-0.0157-0.01930.04820.03090.106431.530930.8984-4.2316
220.04480.07350.0660.10730.10930.10910.0886-0.13490.15620.118-0.07450.02670.18810.0373-0.01270.1649-0.00850.00180.17160.01050.202847.885326.2863-5.6843
230.14040.01410.1461-0.0066-0.00750.04860.07820.0716-0.02550.02490.0063-0.03190.1216-0.00150.01460.2008-0.05240.00320.11270.01250.151121.4698-2.32730.9996
240.14270.0929-0.00620.0596-0.05420.0285-0.05910.0072-0.0831-0.0044-0.02880.00740.0328-0.0614-0.00450.20310.01490.01650.07890.01770.212652.5182-17.87075.1332
250.0575-0.0045-0.0120.0511-0.02780.0111-0.15370.16180.06620.08070.0533-0.25090.1331-0.1653-0.00620.25860.02560.04720.29960.08870.226334.1147-18.414923.6883
260.0832-0.00080.00170.1516-0.07830.0669-0.022-0.03650.02340.00590.0138-0.0604-0.0326-0.006-00.14410.0048-0.02160.14140.02670.162354.5736-7.14737.8609
270.176-0.08850.11760.15560.02590.15670.00530.09980.03440.0591-0.0175-0.01770.0292-0.00100.1183-0.02020.01050.22660.02860.153343.749818.8441-30.2043
280.0802-0.0149-0.02510.0028-0.03930.04330.0380.156-0.016-0.02490.0250.0367-0.0010.02960.00870.2171-0.0203-0.01620.14340.01420.190835.1153-7.7189-13.9768
290.0821-0.05620.07930.0771-0.06580.06710.09430.0579-0.1596-0.0608-0.00660.08250.05950.10580.02430.3393-0.07690.02320.2216-0.02560.226429.045-13.6447-19.7207
300.0138-0.00120.02050.02020.00380.0229-0.00440.0487-0.11250.01130.06020.0646-0.02210.0876-0.00020.1771-0.05320.00570.1578-0.00560.161710.4265-5.9071-16.8877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 196 )
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 302 )
4X-RAY DIFFRACTION4chain 'A' and (resid 303 through 391 )
5X-RAY DIFFRACTION5chain 'A' and (resid 392 through 581 )
6X-RAY DIFFRACTION6chain 'A' and (resid 582 through 861 )
7X-RAY DIFFRACTION7chain 'A' and (resid 862 through 934 )
8X-RAY DIFFRACTION8chain 'A' and (resid 935 through 1017 )
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 85 )
10X-RAY DIFFRACTION10chain 'B' and (resid 86 through 302 )
11X-RAY DIFFRACTION11chain 'B' and (resid 303 through 397 )
12X-RAY DIFFRACTION12chain 'B' and (resid 398 through 842 )
13X-RAY DIFFRACTION13chain 'B' and (resid 843 through 948 )
14X-RAY DIFFRACTION14chain 'B' and (resid 949 through 1018 )
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 85 )
16X-RAY DIFFRACTION16chain 'C' and (resid 86 through 302 )
17X-RAY DIFFRACTION17chain 'C' and (resid 303 through 375 )
18X-RAY DIFFRACTION18chain 'C' and (resid 376 through 581 )
19X-RAY DIFFRACTION19chain 'C' and (resid 582 through 807 )
20X-RAY DIFFRACTION20chain 'C' and (resid 808 through 896 )
21X-RAY DIFFRACTION21chain 'C' and (resid 897 through 966 )
22X-RAY DIFFRACTION22chain 'C' and (resid 967 through 1017 )
23X-RAY DIFFRACTION23chain 'D' and (resid 3 through 108 )
24X-RAY DIFFRACTION24chain 'D' and (resid 109 through 302 )
25X-RAY DIFFRACTION25chain 'D' and (resid 303 through 397 )
26X-RAY DIFFRACTION26chain 'D' and (resid 398 through 581 )
27X-RAY DIFFRACTION27chain 'D' and (resid 582 through 807 )
28X-RAY DIFFRACTION28chain 'D' and (resid 808 through 879 )
29X-RAY DIFFRACTION29chain 'D' and (resid 880 through 943 )
30X-RAY DIFFRACTION30chain 'D' and (resid 944 through 1018 )

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