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- PDB-2hqu: Human dUTPase in complex with alpha,beta-iminodUTP and magnesium ion -

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Basic information

Entry
Database: PDB / ID: 2hqu
TitleHuman dUTPase in complex with alpha,beta-iminodUTP and magnesium ion
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / jelly-roll / protein-substrate analogue ligand complex
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 / RNA binding / extracellular exosome / nucleoplasm / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBarabas, O. / Varga, B. / Vertessy, B.G.
Citation
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.
#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.
History
DepositionJul 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 19, 2016Group: Refinement description
Revision 1.4Aug 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_ncs_dom_lim / 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.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.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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The protein used in this study is an isoform SWS P33316-2 of the protein in the database reference

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,84711
Polymers53,3133
Non-polymers1,5348
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15270 Å2
ΔGint-107 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.409, 71.773, 76.475
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 3 / Auth seq-ID: 24 - 146 / Label seq-ID: 24 - 146

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsthe biological assembly is the trimer found in the asymmetric unit

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Components

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


Mass: 17771.068 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUTN / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P33316, dUTP diphosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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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: 1.68 Å3/Da / Density % sol: 26.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18-20% PEG 3350, 0.1M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Temp details: 293

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8124 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Details: mirror
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8124 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 21420 / Num. obs: 21420 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 1.2 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 0.116 / Net I/σ(I): 9.21
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 3.69 / Num. unique all: 2736 / Rsym value: 0.33 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q5U truncated at residue 146

1q5u


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9 / SU B: 16.788 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25065 945 5.1 %RANDOM
Rwork0.19968 ---
all0.20223 17739 --
obs0.20223 17739 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.252 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å20 Å2
2---0.92 Å20 Å2
3---3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 89 152 3263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223170
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.994309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5365398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17622.609138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46815457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0481527
X-RAY DIFFRACTIONr_chiral_restr0.0860.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022429
X-RAY DIFFRACTIONr_nbd_refined0.210.21450
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2248
X-RAY DIFFRACTIONr_metal_ion_refined0.1180.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.29
X-RAY DIFFRACTIONr_mcbond_it0.4971.52022
X-RAY DIFFRACTIONr_mcangle_it0.86323147
X-RAY DIFFRACTIONr_scbond_it1.57131284
X-RAY DIFFRACTIONr_scangle_it2.2564.51162
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
480tight positional0.050.05
419loose positional0.455
480tight thermal0.130.5
419loose thermal1.2810
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 65 -
Rwork0.246 1291 -
obs-1356 98.98 %
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)
11.215-0.60080.28641.928-0.39951.06750.0074-0.0368-0.14910.01220.0380.34910.0578-0.033-0.0454-0.10440.00640.0313-0.07330.0019-0.097530.20752.01896.3531
20.5785-0.67880.39972.7506-0.59130.28380.06860.1175-0.21710.07260.06930.1962-0.04990.0418-0.1379-0.04650.00760.014-0.0119-0.0321-0.065629.68142.16195.912
30.4607-0.38050.08460.8726-0.15310.52550.04960.03760-0.0374-0.00850.12820.0562-0.0077-0.0411-0.00470.01290.0195-0.0137-0.0046-0.089331.17121.82663.741
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 141
2X-RAY DIFFRACTION1B24 - 141
3X-RAY DIFFRACTION1C24 - 135
4X-RAY DIFFRACTION2A777
5X-RAY DIFFRACTION2A997
6X-RAY DIFFRACTION2B777
7X-RAY DIFFRACTION2C998
8X-RAY DIFFRACTION2C777
9X-RAY DIFFRACTION2B999
10X-RAY DIFFRACTION2C999
11X-RAY DIFFRACTION2A998
12X-RAY DIFFRACTION3A999 - 1049
13X-RAY DIFFRACTION3C1000 - 1043
14X-RAY DIFFRACTION3B1000 - 1056

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