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- PDB-7b7v: Structure of NUDT15 in complex with Acyclovir monophosphate -

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Basic information

Entry
Database: PDB / ID: 7b7v
TitleStructure of NUDT15 in complex with Acyclovir monophosphate
ComponentsProbable 8-oxo-dGTP diphosphatase NUDT15
KeywordsHYDROLASE / Nucleoside Triphosphate Pyrophosphohydrolase / complex / antiviral HYDROLASE
Function / homology
Function and homology information


nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection ...nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / Phosphate bond hydrolysis by NUDT proteins / Azathioprine ADME / xenobiotic catabolic process / regulation of proteasomal protein catabolic process / response to reactive oxygen species / mitotic cell cycle / metal ion binding / cytosol
Similarity search - Function
NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
Chem-4DG / Nucleotide triphosphate diphosphatase NUDT15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRehling, D. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-03406 Sweden
CitationJournal: Nat Commun / Year: 2021
Title: NUDT15 polymorphism influences the metabolism and therapeutic effects of acyclovir and ganciclovir.
Authors: Nishii, R. / Mizuno, T. / Rehling, D. / Smith, C. / Clark, B.L. / Zhao, X. / Brown, S.A. / Smart, B. / Moriyama, T. / Yamada, Y. / Ichinohe, T. / Onizuka, M. / Atsuta, Y. / Yang, L. / Yang, ...Authors: Nishii, R. / Mizuno, T. / Rehling, D. / Smith, C. / Clark, B.L. / Zhao, X. / Brown, S.A. / Smart, B. / Moriyama, T. / Yamada, Y. / Ichinohe, T. / Onizuka, M. / Atsuta, Y. / Yang, L. / Yang, W. / Thomas, P.G. / Stenmark, P. / Kato, M. / Yang, J.J.
History
DepositionDec 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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: Probable 8-oxo-dGTP diphosphatase NUDT15
B: Probable 8-oxo-dGTP diphosphatase NUDT15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,04910
Polymers37,2702
Non-polymers7788
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
  • Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-73 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.643, 49.120, 135.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Probable 8-oxo-dGTP diphosphatase NUDT15 / 8-oxo-dGTPase NUDT15 / 7 / 8-dihydro-8-oxoguanine-triphosphatase NUDT15 / MutT homolog 2 / MTH2 / ...8-oxo-dGTPase NUDT15 / 7 / 8-dihydro-8-oxoguanine-triphosphatase NUDT15 / MutT homolog 2 / MTH2 / Nucleoside diphosphate-linked moiety X motif 15 / Nudix motif 15


Mass: 18635.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT15, MTH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NV35, nucleotide diphosphatase
#2: Chemical ChemComp-4DG / 2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methoxy]ethyl dihydrogen phosphate / acyclic guanosine monophosphate / acyclovir monophosphate


Type: DNA OH 3 prime terminus / Mass: 305.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12N5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH 8.5, 0.2 M MgCl2, 34% PEG 4000 in a 1:2 ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.6→44.09 Å / Num. obs: 41732 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 25.08 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.5
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 2014 / CC1/2: 0.639

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LPG

5lpg


Resolution: 1.6→44.09 Å / SU ML: 0.1761 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3679
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2091 2084 5.01 %
Rwork0.1883 39530 -
obs0.1893 41614 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.73 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 46 233 2772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01292699
X-RAY DIFFRACTIONf_angle_d1.45243682
X-RAY DIFFRACTIONf_chiral_restr0.1025363
X-RAY DIFFRACTIONf_plane_restr0.0085480
X-RAY DIFFRACTIONf_dihedral_angle_d15.6275974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.24161060.27182604X-RAY DIFFRACTION98.37
1.64-1.680.26921390.25142569X-RAY DIFFRACTION98.69
1.68-1.720.28921500.24382567X-RAY DIFFRACTION98.48
1.72-1.770.2731650.23852542X-RAY DIFFRACTION98.87
1.77-1.830.26871680.23012577X-RAY DIFFRACTION99.56
1.83-1.90.25421300.22722621X-RAY DIFFRACTION99.71
1.9-1.970.24221440.21372625X-RAY DIFFRACTION99.86
1.97-2.060.21791470.20172613X-RAY DIFFRACTION99.64
2.06-2.170.24251210.1982644X-RAY DIFFRACTION99.96
2.17-2.310.24561510.20412619X-RAY DIFFRACTION99.75
2.31-2.490.23461390.20542662X-RAY DIFFRACTION99.86
2.49-2.740.21571080.19652695X-RAY DIFFRACTION99.54
2.74-3.130.21561330.18872681X-RAY DIFFRACTION99.93
3.13-3.940.16861190.16962722X-RAY DIFFRACTION99.61
3.95-44.090.1741640.15722789X-RAY DIFFRACTION97.78
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)
12.495681827980.380821890790.8090524186730.833460757303-0.7735172590841.69091836773-0.1588180681470.07917324033090.081147052891-0.09103696554720.0937259095063-0.103463972955-0.5097279863260.113711912818-0.004164863765550.2238581028590.03247747923450.006208223133270.156013017832-0.01937019186670.168390038766-8.92983481281-6.2178672306421.3523045859
23.094746766711.383264361171.632414147832.362615406530.3861304253461.72887053395-0.06445261084060.14342106835-0.239670178476-0.04597494010080.161313367282-0.322405000771-0.1017210946920.2178132013010.02101682902130.1685260036330.05087528579490.02896556795980.165741156-0.01602178366690.212832239592-8.52004700601-13.851289564921.3174768174
31.857017589580.5090266594740.4541681279780.944538228560.3850454214320.978906515891-0.1926782651420.09193674686040.104532085525-0.2039667638820.283945566625-0.304393805831-0.6111141017230.3372921230360.0002298486813320.338199617526-0.04193208864390.01521979298810.264726761707-0.01677622404970.289413612581-3.24459806782-3.5844515944619.2273020426
41.239912309870.7783521687190.5235240638131.29648688055-0.2932765813670.604322835446-0.1847390658680.1420413944470.119014920208-0.3552860903190.1065306444760.15874799443-0.466748038541-0.0140252627602-2.63730136395E-70.3607143722260.0832947916505-0.01941770583120.2567419538250.03662723730420.255877556599-20.3139588534-8.1761151092312.5435381111
51.731633742090.8337533961180.3666861381972.358725286511.87262264223.352863992180.385568532155-0.268849896285-0.3267936063780.170483972734-0.0829642599347-0.1831450745970.602588099497-0.5770248976780.0517237407640.258916282174-0.0339651622605-0.06393180260880.3041000203650.07119710435170.23968921781-26.1059337444-31.524786198712.5329925752
61.045695022871.365299267970.9083873854892.02957673711.534487427231.787383998560.1227831760460.0653265901735-0.232778744712-0.1131684194690.0434124290743-0.1345939144820.170719038506-0.2299184458130.01764759988060.1918491917980.0474229786382-0.01345810715460.1911228037610.03110658469050.219272041359-23.8603806633-27.195758590210.525347074
71.66759271591-0.2734211037730.8913432678061.32163568043-1.009752441762.304584520080.697062218566-0.710803033632-0.3912849745770.0188353150415-0.3520848897590.2621119144410.97620004286-1.221851037540.387258216180.380110314725-0.283704200145-0.1049544197540.5903578836740.1178092775220.34630401923-33.7702127315-35.695761254612.2974940665
81.488536936010.9820267211241.040667192110.7316340259231.143433477872.921285068460.339917125149-0.641705275082-0.1675954460340.177664086767-0.4572013941060.1511976760640.278092930227-1.599708634740.03013224511850.1928420651310.04200761643830.02773740837180.535387642711-0.001890401700820.265285142484-27.9770938976-21.667726894422.0125186568
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 11:34)AA11 - 341 - 24
22(chain A and resid 35:104)AA35 - 10425 - 95
33(chain A and resid 105:139)AA105 - 13996 - 131
44(chain A and resid 140:164)AA140 - 164132 - 158
55(chain B and resid 10:54)BF10 - 541 - 45
66(chain B and resid 55:104)BF55 - 10446 - 97
77(chain B and resid 105:135)BF105 - 13598 - 128
88(chain B and resid 136:164)BF136 - 164129 - 159

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