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- PDB-3ehw: Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: vis... -

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Basic information

Entry
Database: PDB / ID: 3ehw
TitleHuman dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site
ComponentsdUTP pyrophosphatase
KeywordsHYDROLASE / jelly-roll / full-length C-terminal arm / enzyme-ligand complex
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / signaling receptor inhibitor activity / dTMP biosynthetic process ...pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / signaling receptor inhibitor activity / dTMP biosynthetic process / regulation of protein-containing complex assembly / liver development / DNA replication / magnesium ion binding / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial / Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTakacs, E. / Barabas, O. / Vertessy, B.G.
Citation
Journal: To be Published
Title: Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site
Authors: Takacs, E. / Barabas, O. / Vertessy, B.G.
#1: Journal: Structure / Year: 1996
Title: Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits.
Authors: Mol, C.D. / Harris, J.M. / McIntosh, E.M. / Tainer, J.A.
#2: Journal: FEBS Lett. / Year: 2007
Title: Active site closure facilitates juxtaposition of reactant atoms for initiation of catalysis by human dUTPase.
Authors: Varga, B. / Barabas, O. / Kovari, J. / Toth, J. / Hunyadi-Gulyas, E. / Klement, E. / Medzihradszky, K.F. / Tolgyesi, F. / Fidy, J. / Vertessy, B.G.
History
DepositionSep 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dUTP pyrophosphatase
B: dUTP pyrophosphatase
C: dUTP pyrophosphatase
X: dUTP pyrophosphatase
Y: dUTP pyrophosphatase
Z: dUTP pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,62420
Polymers106,6266
Non-polymers2,99714
Water13,169731
1
A: dUTP pyrophosphatase
B: dUTP pyrophosphatase
C: dUTP pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,81210
Polymers53,3133
Non-polymers1,4997
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16640 Å2
ΔGint-93 kcal/mol
Surface area14140 Å2
MethodPISA
2
X: dUTP pyrophosphatase
Y: dUTP pyrophosphatase
Z: dUTP pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,81210
Polymers53,3133
Non-polymers1,4997
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16270 Å2
ΔGint-93 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.446, 87.160, 70.608
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
dUTP pyrophosphatase


Mass: 17771.068 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUT / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6FHN1, UniProt: P33316*PLUS, dUTP diphosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES buffer, containing 20% PEG 3350 and 200 mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8031 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 7, 2004 / Details: BENT, VERTICALLY FOCUSING MIRROR
RadiationMonochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8031 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 70417 / Num. obs: 70417 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.17 % / Biso Wilson estimate: 26.26 Å2 / Rsym value: 0.071 / Net I/σ(I): 10.15
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.13 % / Mean I/σ(I) obs: 2.24 / Num. unique all: 10689 / Rsym value: 0.475 / % possible all: 97.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q5U

1q5u


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.299 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19898 3574 5.1 %RANDOM
Rwork0.1576 ---
obs0.15972 66842 95.84 %-
all-66842 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0.07 Å2
2--0.24 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6346 0 176 731 7253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226678
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9959069
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.11622.933283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.382151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1461553
X-RAY DIFFRACTIONr_chiral_restr0.0790.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025096
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.23386
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.24585
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2902
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0160.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.87524251
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5246640
X-RAY DIFFRACTIONr_scbond_it3.44662710
X-RAY DIFFRACTIONr_scangle_it5.14202421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 247 -
Rwork0.235 5060 -
obs--97.36 %
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)
11.21780.371-0.15030.6834-0.20310.75770.0096-0.1530.09110.0638-0.01980.02860.0336-0.0150.0102-0.0422-0.0056-0.0028-0.0495-0.022-0.0658-10.6739-0.038732.4647
20.6136-0.2207-0.23410.5974-0.16670.80730.01940.0089-0.0482-0.0456-0.003-0.0076-0.01180.0077-0.0163-0.05240.0034-0.0047-0.05520.0206-0.040622.179912.5621.0126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 164
2X-RAY DIFFRACTION1B24 - 164
3X-RAY DIFFRACTION1C24 - 164
9X-RAY DIFFRACTION2X24 - 164
10X-RAY DIFFRACTION2Y24 - 164
11X-RAY DIFFRACTION2Z24 - 164

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