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- PDB-8c8i: Human dUTPase in complex with a potent proteinaceous inhibitor (Stl) -

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Basic information

Entry
Database: PDB / ID: 8c8i
TitleHuman dUTPase in complex with a potent proteinaceous inhibitor (Stl)
Components
  • Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
  • Orf20
KeywordsHYDROLASE / Inhibitor / Complex / dUTPase
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / nucleobase-containing compound metabolic process / dTMP biosynthetic process / DNA replication / magnesium ion binding / mitochondrion ...dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / nucleobase-containing compound metabolic process / dTMP biosynthetic process / DNA replication / magnesium ion binding / mitochondrion / DNA binding / RNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial / Orf20
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKohegyi, B.K. / Nyiri, K. / Vertessy, B.G.
Funding support Hungary, 1items
OrganizationGrant numberCountry
Hungarian National Research, Development and Innovation OfficePD134324 Hungary
CitationJournal: Sci Rep / Year: 2025
Title: Full-length inhibitor protein is the most effective to perturb human dUTPase activity.
Authors: Kohegyi, B. / Toth, Z.S. / Gal, E. / Laczkovich, M. / Benedek, A. / Vertessy, B.G. / Nyiri, K.
History
DepositionJan 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
D: Orf20
E: Orf20
F: Orf20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1877
Polymers94,1636
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.450, 82.660, 139.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d_1ens_1
d_2ens_1
d_3ens_1
d_1ens_2
d_2ens_2
d_3ens_2

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.140034690694, 0.898545046119, 0.415941204376), (0.264957893786, 0.438766588366, -0.858650799484), (-0.954037525427, -0.0100339936699, -0.29951914638)11.1085615739, 9.26251166483, 34.9906048298
2given(-0.136692629585, 0.261217579129, -0.955552458723), (0.90025502466, 0.435252671726, -0.00979807787136), (0.413347330451, -0.861580227321, -0.294658270372)32.3750513231, -13.7041274144, 13.8695549527
3given(-0.135668353987, 0.276996457811, -0.951245005289), (0.89419766505, 0.447663442328, 0.0028245745787), (0.426620010718, -0.850217857236, -0.308423348162)32.1591077681, -13.9063838269, 13.855041465
4given(-0.14605442653, 0.91005222884, 0.387908552722), (0.232526613754, 0.412708347698, -0.880683367412), (-0.961560959267, -0.0384286419708, -0.271889244158)11.3312029569, 10.52337427, 34.8784911208

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Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial / dUTPase / dUTP pyrophosphatase


Mass: 14178.108 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUT / Production host: Escherichia coli (E. coli) / References: UniProt: P33316, dUTP diphosphatase
#2: Protein Orf20


Mass: 17209.420 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F0J8
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: Ammonium sulfate, Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2021
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→71.1 Å / Num. obs: 15601 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 73.54 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.6
Reflection shellResolution: 3.2→3.37 Å / Rmerge(I) obs: 1.077 / Num. unique obs: 2232 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→52.69 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 765 4.92 %
Rwork0.1932 --
obs0.196 15550 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→52.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6110 0 1 0 6111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046255
X-RAY DIFFRACTIONf_angle_d0.6948529
X-RAY DIFFRACTIONf_dihedral_angle_d4.871922
X-RAY DIFFRACTIONf_chiral_restr0.044955
X-RAY DIFFRACTIONf_plane_restr0.0051115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.28851500.21292900X-RAY DIFFRACTION100
3.45-3.790.26051630.20362888X-RAY DIFFRACTION100
3.79-4.340.24441340.1722963X-RAY DIFFRACTION100
4.34-5.470.21081580.16372940X-RAY DIFFRACTION100
5.47-52.690.26831600.21773094X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.1913 Å / Origin y: 8.7573 Å / Origin z: 11.2703 Å
111213212223313233
T0.3471 Å20.0256 Å20.0555 Å2-0.3196 Å2-0.02 Å2--0.3405 Å2
L1.4925 °2-0.0003 °20.6088 °2-1.5077 °20.6532 °2--2.213 °2
S0.17 Å °-0.0046 Å °0.2239 Å °-0.0018 Å °-0.071 Å °-0.1787 Å °0.3061 Å °-0.106 Å °-0.0668 Å °
Refinement TLS groupSelection details: all

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