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- SASDC87: Deoxyuridine 5'-triphosphate nucleotidohydrolase complex with SaP... -

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Basic information

Entry
Database: SASBDB / ID: SASDC87
SampleDeoxyuridine 5'-triphosphate nucleotidohydrolase complex with SaPIbov1 pathogenicity island repressor [3:2] (SEC-SAXS)
  • Deoxyuridine 5'-triphosphate nucleotidohydrolase (protein), hDUT, Homo sapiens
  • SaPIbov1 pathogenicity island repressor (protein), Stl, Staphylococcus aureus
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / signaling receptor inhibitor activity / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / nucleobase-containing compound metabolic process / peroxisome proliferator activated receptor binding / dTMP biosynthetic process ...pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / signaling receptor inhibitor activity / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / nucleobase-containing compound metabolic process / peroxisome proliferator activated receptor binding / dTMP biosynthetic process / regulation of protein-containing complex assembly / liver development / response to organic cyclic compound / DNA replication / magnesium ion binding / mitochondrion / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / Helix-turn-helix / dUTPase-like superfamily / 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
Stl / Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
CitationDate: 2018 Mar 12
Title: Structural model of human dUTPase in complex with a novel proteinaceous inhibitor
Authors: Nyíri K / Mertens H / Tihanyi B / Nagy G / Kőhegyi B / Matejka J / Harris M / Szabó J / Papp-Kádár V / Németh-Pongrácz V / Ozohanics O / Vékey K / Svergun D / Borysik A
Contact author
  • Haydyn Mertens (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #1493
Type: dummy / Software: (2.9.0) / Radius of dummy atoms: 2.90 A / Symmetry: P2 / Chi-square value: 1.037
Search similar-shape structures of this assembly by Omokage search (details)
Model #1494
Type: atomic / Software: (2.9.0) / Radius of dummy atoms: 1.90 A / Symmetry: P1 / Chi-square value: 1.22
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Deoxyuridine 5'-triphosphate nucleotidohydrolase complex with SaPIbov1 pathogenicity island repressor [3:2] (SEC-SAXS)
Dry vol: 149667 / Entity id: 775 / 776
BufferName: 50 mM HEPES 300 mM NaCl 5 mM MgCl2 / pH: 7.5 / Comment: Buffer B
Entity #775Name: hDUT / Type: protein
Description: Deoxyuridine 5'-triphosphate nucleotidohydrolase
Formula weight: 18.029 / Num. of mol.: 3 / Source: Homo sapiens / References: UniProt: P33316
Sequence:
GSHMPCSEET PAISPSKRAR PAEVGGMQLR FARLSEHATA PTRGSARAAG YDLYSAYDYT IPPMEKAVVK TDIQIALPSG CYGRVAPRSG LAAKHFIDVG AGVIDEDYRG NVGVVLFNFG KEKFEVKKGD RIAQLICERI FYPEIEEVQA LDDTERGSGG FGSTGKN
Entity #776Name: Stl / Type: protein / Description: SaPIbov1 pathogenicity island repressor / Formula weight: 32.016 / Num. of mol.: 2 / Source: Staphylococcus aureus / References: UniProt: E2FZP6
Sequence: GSPEFSMEGA GQMAELPTHY GTIIKTLRKY MKLTQSKLSE RTGFSQNTIS NHENGNRNIG VNEIEIYGKG LGIPSYILHR ISDEFKEKGY SPTLNDFGKF DKMYSYVNKA YYNDGDIYYS SYDLYDETIK LLELLKESKI NVNDIDYDYV LKLYKQILST DTEKSIINYE ...Sequence:
GSPEFSMEGA GQMAELPTHY GTIIKTLRKY MKLTQSKLSE RTGFSQNTIS NHENGNRNIG VNEIEIYGKG LGIPSYILHR ISDEFKEKGY SPTLNDFGKF DKMYSYVNKA YYNDGDIYYS SYDLYDETIK LLELLKESKI NVNDIDYDYV LKLYKQILST DTEKSIINYE TLANTRKSSD KKREVTIEEI GEFHEKYLKL LFTNLETHND RKKALAEIEK LKEESIYLGE KLRLVPNHHY DAIKGKPMYK LYLYEYPDRL EHQKKIILEK DTN

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Experimental information

BeamInstrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3.1 mm
DetectorName: Pilatus 2M
Scan
Title: hDUTstl_SEC_2 / Measurement date: Jul 10, 2016 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 3600 / Unit: 1/nm /
MinMax
Q0.1653 5.0307
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1200 /
MinMax
Q0.165303 3.4686
P(R) point1 1200
R0 14
Result
Type of curve: single_conc / Standard: water
ExperimentalExperimental errorStandardStandard errorPorodPorod errorEstimatedEstimated errorEstimated method
MW121 kDa3 121 kDa3 112 kDa6 ---
Volume----190 nm320 242 20 DAM volume

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.047 0.001 0.046 0.001
Radius of gyration, Rg3.88 nm0.1 3.8 nm0.1

MinMaxError
D-14 0.5
Guinier point1 65 -

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